diff --git a/README.md b/README.md index d6aca64a..e22cdb60 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Steps include: - Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq - Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html) - Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html) -- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollectHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics) +- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`riker multi`](https://github.com/fulcrumgenomics/riker) - QC aggregation using [`multiqc`](https://multiqc.info/) diff --git a/assets/schema_input.json b/assets/schema_input.json index 8f666f27..248fed5a 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -89,12 +89,6 @@ "description": "Whether to run coverage analysis for the sample", "default": true }, - "disable_picard_metrics": { - "meta": ["disable_picard_metrics"], - "type": "boolean", - "description": "Whether to disable Picard metrics calculation. This can be used to speed up processing if Picard is not needed.", - "default": true - }, "roi": { "meta": ["roi"], "type": "string", diff --git a/assets/schema_sampleinfo.json b/assets/schema_sampleinfo.json index 092cc130..c1938956 100644 --- a/assets/schema_sampleinfo.json +++ b/assets/schema_sampleinfo.json @@ -129,12 +129,6 @@ "description": "Whether to run coverage analysis for the sample", "default": true }, - "disable_picard_metrics": { - "meta": ["disable_picard_metrics"], - "type": "boolean", - "description": "Whether to disable Picard metrics calculation. This can be used to speed up processing if Picard is not needed.", - "default": true - }, "roi": { "meta": ["roi"], "type": "string", diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index c8184a2d..1280a9e1 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } -process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt' } } +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } +process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-9b10d606ce2f36b6_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index 2f7b575a..d08dd327 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } -process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-039d1ec6b47ba325_1.txt' } } +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } +process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-077315907ed11315_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 78d2a3f2..00c5e960 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } -process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } +process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index cb309025..14270ce7 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } -process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:039d1ec6b47ba325' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } +process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:077315907ed11315' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index a53b4e19..df7923dd 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } -process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } +process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 06c0dd3f..e486ec26 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } -process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b047611068a4009d62d8352e8bb4ab27fa993708a82c029f115e6758b2e44bec/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } +process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/053f6d8c55b57e04b654070a3bd6eaa90685590158019d35c16092d301b80cb1/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index fe83b990..31457ab0 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } -process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9ebe780f2738c655' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } +process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:a26da1aa4e8d32a6' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index fffe6e07..bad6f0f2 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1,2 +1,2 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } -process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:fc57bb53140baade' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } +process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d1ed21d66511158d' } } diff --git a/conf/modules.config b/conf/modules.config index 95978df0..d98252e1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -257,13 +257,6 @@ process { memory = 1.GB } - //// Picard - withName: '.*BAM_QC:PICARD_.*$' { - cpus = 1 - memory = { 16.GB * task.attempt } - ext.args = "--MAX_RECORDS_IN_RAM 50000000" - } - withName: '.*MD5SUM' { cpus = 1 memory = 128.MB diff --git a/docs/images/metro_map_dark.md b/docs/images/metro_map_dark.md index 65349f39..b3c4b3b6 100644 --- a/docs/images/metro_map_dark.md +++ b/docs/images/metro_map_dark.md @@ -39,7 +39,7 @@ graph TD SAMTOOLS_COV -->|qc| MULTIQC_LIBRARY CRAM_OUT -->|qc| SAMTOOLS_QC - CRAM_OUT -->|qc| PICARD + CRAM_OUT -->|qc| RIKER SAMTOOLS_QC -->|qc| MULTIQC_LIBRARY - PICARD -->|qc| MULTIQC_LIBRARY + RIKER -->|qc| MULTIQC_LIBRARY ``` diff --git a/docs/images/metro_map_dark.svg b/docs/images/metro_map_dark.svg index 0f452bc5..8b88840b 100644 --- a/docs/images/metro_map_dark.svg +++ b/docs/images/metro_map_dark.svg @@ -87,7 +87,7 @@ MOSDEPTH SAMTOOLS_COV SAMTOOLS_QC -PICARD +RIKER MULTIQC_LIBRARY diff --git a/docs/images/metro_map_light.md b/docs/images/metro_map_light.md index 5cd6a5b0..eb93ce46 100644 --- a/docs/images/metro_map_light.md +++ b/docs/images/metro_map_light.md @@ -39,7 +39,7 @@ graph TD SAMTOOLS_COV -->|qc| MULTIQC_LIBRARY CRAM_OUT -->|qc| SAMTOOLS_QC - CRAM_OUT -->|qc| PICARD + CRAM_OUT -->|qc| RIKER SAMTOOLS_QC -->|qc| MULTIQC_LIBRARY - PICARD -->|qc| MULTIQC_LIBRARY + RIKER -->|qc| MULTIQC_LIBRARY ``` diff --git a/docs/images/metro_map_light.svg b/docs/images/metro_map_light.svg index ac3be697..c6487f66 100644 --- a/docs/images/metro_map_light.svg +++ b/docs/images/metro_map_light.svg @@ -92,7 +92,7 @@ MOSDEPTH SAMTOOLS_COV SAMTOOLS_QC -PICARD +RIKER MULTIQC_LIBRARY diff --git a/docs/output.md b/docs/output.md index 119dd95e..23e7abd8 100644 --- a/docs/output.md +++ b/docs/output.md @@ -16,15 +16,6 @@ A separate directory will be created in the output directory for each sample con Output files - `SAMPLE` - - `SAMPLE.CollectHsMetrics.coverage_metrics`: The coverage metrics calculated by `picard CollectHsMetrics` - - `SAMPLE.CollectMultipleMetrics.alignment_summary_metrics`: The alignment summary metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.base_distribution_by_cycle_metrics`: The base distribution by cycle metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.base_distribution_by_cycle.pdf`: PDF file containing the base distribution by cycle metrics - - `SAMPLE.CollectMultipleMetrics.quality_by_cycle_metrics`: The quality by cycle metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.quality_by_cycle.pdf`: PDF file containing the quality by cycle metrics - - `SAMPLE.CollectMultipleMetrics.quality_distribution_metrics`: The quality by distribution metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.quality_distribution.pdf`: PDF file containing the quality distribution metrics - - `SAMPLE.CollectMultipleMetrics.read_length_histogram.pdf`: A histogram detailing the read lengths made with `picard CollectMultipleMetrics` - `SAMPLE.coverage.txt`: The coverage metrics calculated by `samtools coverage` - `SAMPLE.cram`: The CRAM file generated by the aligner - `SAMPLE.cram.crai`: The index of the CRAM file diff --git a/docs/usage.md b/docs/usage.md index f59c809a..09ab7485 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -32,7 +32,6 @@ A `fastq` samplesheet file consisting of paired-end data may look something like adapter_R1: AGATCGGAAGAGCACACGTCTGAACTCCTTA adapter_R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT run_coverage: true - disable_picard_metrics: false roi: null tag: WES sample_type: DNA @@ -42,28 +41,27 @@ A `fastq` samplesheet file consisting of paired-end data may look something like Following table shows the fields that are used by the `fastq` samplesheet: -| Column | Description | Required | -| ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- | -| `id` | Unique sample identifier | :heavy_check_mark: | -| `samplename` | The sample name corresponding to the sample in the Fastq file(s) | :heavy_check_mark: | -| `genome` | The genome build to use for the analysis. Currently supports `GRCh38`, `GRCm39` and `GRCz11` | :heavy_check_mark: (unless `organism` is given) | -| `organism` | Full name of the organism. Currently supports `Homo sapiens`, `Mus musculus` and `Danio rerio` | :heavy_check_mark: (unless `genome` is given) | -| `library` | Sample library name | :x: | -| `tag` | The tag used by the sample. Can be one of `WES`, `WGS`, `SeqCap` and `coPGT-M` | :x: | -| `aligner` | The aligner to use for this sample. Can be one of these: `bowtie2`, `bwamem`, `bwamem2`, `dragmap`, `strobe` and `snap`. Set to `false` to output fastq. | :heavy_check_mark: | -| `markdup` | Markdup algorithm to use for duplicate marking. Can be set to `bamsormadup`, `samtools` or `false` | :x: | -| `umi_aware` | Whether UMI-aware processing should be used. Only applies when `markdup` is set to `samtools` | :x: | -| `skip_trimming` | Skip adapter trimming step | :x: | -| `trim_front` | Number of bases to trim from the front of reads | :x: | -| `trim_tail` | Number of bases to trim from the tail of reads | :x: | -| `adapter_R1` | Adapter sequence for read 1 | :x: | -| `adapter_R2` | Adapter sequence for read 2 | :x: | -| `run_coverage` | Run coverage analysis | :x: | -| `disable_picard_metrics` | Disable Picard metrics collection | :x: | -| `roi` | The path to a BED file containing Regions Of Interest for coverage analysis | :x: | -| `sample_type` | Sample type (e.g., `DNA`, `RNA`) | :x: | -| `fastq_1` | FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :heavy_check_mark: | -| `fastq_2` | FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :x: | +| Column | Description | Required | +| --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- | +| `id` | Unique sample identifier | :heavy_check_mark: | +| `samplename` | The sample name corresponding to the sample in the Fastq file(s) | :heavy_check_mark: | +| `genome` | The genome build to use for the analysis. Currently supports `GRCh38`, `GRCm39` and `GRCz11` | :heavy_check_mark: (unless `organism` is given) | +| `organism` | Full name of the organism. Currently supports `Homo sapiens`, `Mus musculus` and `Danio rerio` | :heavy_check_mark: (unless `genome` is given) | +| `library` | Sample library name | :x: | +| `tag` | The tag used by the sample. Can be one of `WES`, `WGS`, `SeqCap` and `coPGT-M` | :x: | +| `aligner` | The aligner to use for this sample. Can be one of these: `bowtie2`, `bwamem`, `bwamem2`, `dragmap`, `strobe` and `snap`. Set to `false` to output fastq. | :heavy_check_mark: | +| `markdup` | Markdup algorithm to use for duplicate marking. Can be set to `bamsormadup`, `samtools` or `false` | :x: | +| `umi_aware` | Whether UMI-aware processing should be used. Only applies when `markdup` is set to `samtools` | :x: | +| `skip_trimming` | Skip adapter trimming step | :x: | +| `trim_front` | Number of bases to trim from the front of reads | :x: | +| `trim_tail` | Number of bases to trim from the tail of reads | :x: | +| `adapter_R1` | Adapter sequence for read 1 | :x: | +| `adapter_R2` | Adapter sequence for read 2 | :x: | +| `run_coverage` | Run coverage analysis | :x: | +| `roi` | The path to a BED file containing Regions Of Interest for coverage analysis | :x: | +| `sample_type` | Sample type (e.g., `DNA`, `RNA`) | :x: | +| `fastq_1` | FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :heavy_check_mark: | +| `fastq_2` | FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :x: | An [example samplesheet](../tests/inputs/test.yml) has been provided with the pipeline. @@ -108,7 +106,6 @@ A `flowcell` sample info JSON/YML file consisting for one sequencing run may loo adapter_R1: AGATCGGAAGAGCACACGTCTGAACTCCTTA adapter_R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT run_coverage: true - disable_picard_metrics: false roi: null tag: WES sample_type: DNA diff --git a/main.nf b/main.nf index 8d7667e2..401e4f29 100644 --- a/main.nf +++ b/main.nf @@ -195,10 +195,7 @@ workflow { samtools_stats = PREPROCESSING.out.samtools_stats samtools_flagstat = PREPROCESSING.out.samtools_flagstat samtools_idxstats = PREPROCESSING.out.samtools_idxstats - picard_multiplemetrics = PREPROCESSING.out.picard_multiplemetrics - picard_multiplemetrics_pdf = PREPROCESSING.out.picard_multiplemetrics_pdf - picard_wgsmetrics = PREPROCESSING.out.picard_wgsmetrics - picard_hsmetrics = PREPROCESSING.out.picard_hsmetrics + riker_metrics = PREPROCESSING.out.riker_metrics md5sums = PREPROCESSING.out.md5sums multiqc_report = PREPROCESSING.out.multiqc_report multiqc_data = PREPROCESSING.out.multiqc_data @@ -360,22 +357,7 @@ output { return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") } } - picard_multiplemetrics { - path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") - } - } - picard_multiplemetrics_pdf { - path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") - } - } - picard_wgsmetrics { - path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") - } - } - picard_hsmetrics { + riker_metrics { path { meta, _file -> return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") } diff --git a/modules.json b/modules.json index 328d7a78..4e1e1d7f 100644 --- a/modules.json +++ b/modules.json @@ -68,31 +68,19 @@ }, "multiqc": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] }, "multiqcsav": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] }, - "picard/collecthsmetrics": { + "riker/multi": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff" - }, - "picard/collectmultiplemetrics": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff" - }, - "picard/collectwgsmetrics": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "bdcc0aa910bb7dc54a7335e81608b7a03f0a9992", "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff" + "patch": "modules/nf-core/riker/multi/riker-multi.diff" }, "samtools/convert": { "branch": "master", diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new file mode 100644 index 00000000..2a91c22d --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt @@ -0,0 +1,1526 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: 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f787dbe1..00000000 --- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt +++ /dev/null @@ -1,125 +0,0 @@ - -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-aarch64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958 -https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d -https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6 -https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d -https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1 -https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc -https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f -https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d -https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a -https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261 -https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda#7b9813e885482e3ccb1fa212b86d7fd0 -https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.0-h022381a_0.conda#86db4036fd08bf34e991bf48a8af405d -https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42-h1022ec0_0.conda#a0b5de740d01c390bdbb46d7503c9fab -https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda#182afabe009dc78d8b73100255ee6868 -https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73 -https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda#3b129669089e4d6a5c6871dbb4669b99 -https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 -https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda#3d49cad61f829f4f0e0611547a9cda12 -https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda#7fc6affb9b01e567d2ef1d05b84aa6ed -https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 -https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda#3cfbe780f0f51cc8cba41db9f8a28bfe -https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452 -https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959 -https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f -https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d -https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115 -https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c -https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2 -https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265 -https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda#f56573d05e3b735cb03efeb64a15f388 -https://conda.anaconda.org/conda-forge/linux-aarch64/brotli-python-1.2.0-py314h352cb57_1.conda#a1b5c571a0923a205d663d8678df4792 -https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5 -https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089 -https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c -https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371 -https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda#b866ff7007b934d564961066c8195983 -https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda#a2c1eeadae7a309daed9d62c96012a2b -https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_18.conda#574d88ce3348331e962cfa5ed451b247 -https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_18.conda#41f261f5e4e2e8cbd236c2f1f15dae1b -https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.32-pthreads_h9d3fd7e_0.conda#5d2ce5cf40443d055ec6d33840192265 -https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-6_haddc8a3_openblas.conda#652bb20bb4618cacd11e17ae070f47ce -https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-6_hd72aa62_openblas.conda#939e300b110db241a96a1bed438c315b -https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-6_h88aeb00_openblas.conda#e23a27b52fb320687239e2c5ae4d7540 -https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda#25d896c331481145720a21e5145fad65 -https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102 -https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.5-hfae3067_0.conda#d2bb0c889d94f2fdc5856392c3002976 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 -https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda#f51503ac45a4888bce71af9027a2ecc9 -https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda#b99ed99e42dafb27889483b3098cace7 -https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda#a229e22d4d8814a07702b0919d8e6701 -https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda#0fed1ff55f4938a65907f3ecf62609db -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681 -https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e -https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac -https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9 -https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e -https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac -https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983 -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a -https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda#e5de3c36dd548b35ff2a8aa49208dcb3 -https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda#04558c96691bed63104678757beb4f8d -https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda#e7f6ed9e60043bb5cbcc527764897f0d -https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda#870293df500ca7e18bedefa5838a22ab -https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a -https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc -https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257 -https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e -https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9 -https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552 -https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725 -https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f -https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250 -https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171 -https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c -https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af -https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d -https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c -https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386 -https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43 -https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2 -https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2 -https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3 -https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351 -https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964 -https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2 -https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8 -https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c -https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b -https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684 -https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98 -https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a -https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910 -https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34 -https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372 -https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7 -https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88 -https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58 -https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc -https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240 -https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6 -https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98 -https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c -https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2 -https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac -https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130 -https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59 -https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0 -https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66 -https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9 -https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a -https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864 -https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6 -https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206 -https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b -https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873 -https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f -https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 37e7612d..7a970e2b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.34 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index e80e8cd8..c4bc715e 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,8 +4,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc627..27ce18d8 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370f..44899216 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } diff --git a/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt b/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt deleted file mode 100644 index e2883507..00000000 --- a/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt +++ /dev/null @@ -1,131 +0,0 @@ - -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882 -https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de -https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec -https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6 -https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af -https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb -https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb -https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda#2c21e66f50753a083cbe6b80f38268fa -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda#1b08cd684f34175e4514474793d44bcb -https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-hf4e2dac_0.conda#810d83373448da85c3f673fbcb7ad3a3 -https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 -https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0 -https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 -https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec -https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab -https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 -https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda#a443f87920815d41bfe611296e507995 -https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452 -https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959 -https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f -https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d -https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115 -https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c -https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2 -https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265 -https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda#8910d2c46f7e7b519129f486e0fe927a -https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5 -https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089 -https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c -https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371 -https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda#b866ff7007b934d564961066c8195983 -https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda#a2c1eeadae7a309daed9d62c96012a2b -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda#646855f357199a12f02a87382d429b75 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda#9063115da5bc35fdc3e1002e69b9ef6e -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.32-pthreads_h94d23a6_0.conda#89d61bc91d3f39fda0ca10fcd3c68594 -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-6_h4a7cf45_openblas.conda#6d6d225559bfa6e2f3c90ee9c03d4e2e 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-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda#eba48a68a1a2b9d3c0d9511548db85db -https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda#fb16b4b69e3f1dcfe79d80db8fd0c55d -https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda#e289f3d17880e44b633ba911d57a321b -https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda#867127763fbe935bab59815b6e0b7b5c -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681 -https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e -https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac 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+timestamp: 1764777145593 diff --git a/modules/nf-core/multiqcsav/environment.yml b/modules/nf-core/multiqcsav/environment.yml index b95a2972..b190a347 100644 --- a/modules/nf-core/multiqcsav/environment.yml +++ b/modules/nf-core/multiqcsav/environment.yml @@ -5,9 +5,9 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/multiqc - - bioconda::multiqc=1.34 + - bioconda::multiqc=1.35 # renovate: datasource=conda depName=bioconda/multiqc_sav - bioconda::multiqc_sav=0.2.0 - - pip=25.3 + - pip=26.1.1 - pip: - interop==1.9.0 diff --git a/modules/nf-core/multiqcsav/main.nf b/modules/nf-core/multiqcsav/main.nf index 5d25de8f..09846f59 100644 --- a/modules/nf-core/multiqcsav/main.nf +++ b/modules/nf-core/multiqcsav/main.nf @@ -4,8 +4,8 @@ process MULTIQCSAV { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data' - : 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data' + : 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6'}" input: tuple val(meta), path(xml), path(interop_bin, stageAs: "InterOp/*"), path(extra_multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqcsav/meta.yml b/modules/nf-core/multiqcsav/meta.yml index 1bef87b5..7c3130ad 100644 --- a/modules/nf-core/multiqcsav/meta.yml +++ b/modules/nf-core/multiqcsav/meta.yml @@ -140,24 +140,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt + lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-9b10d606ce2f36b6_1.txt linux/arm64: - lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-039d1ec6b47ba325_1.txt + lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-077315907ed11315_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa - build_id: bd-644a84cef31cc4aa_1 - scan_id: sc-253553e37f233660_1 + name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6 + build_id: bd-9b10d606ce2f36b6_1 + scan_id: sc-e07d8899984fea53_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:039d1ec6b47ba325 - build_id: bd-039d1ec6b47ba325_1 - scan_id: sc-1c30a1d921d59ec5_1 + name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:077315907ed11315 + build_id: bd-077315907ed11315_1 + scan_id: sc-bd28ba4987c53bbe_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9ebe780f2738c655 - build_id: bd-9ebe780f2738c655_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data + name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:a26da1aa4e8d32a6 + build_id: bd-a26da1aa4e8d32a6_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:fc57bb53140baade - build_id: bd-fc57bb53140baade_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b047611068a4009d62d8352e8bb4ab27fa993708a82c029f115e6758b2e44bec/data + name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d1ed21d66511158d + build_id: bd-d1ed21d66511158d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/053f6d8c55b57e04b654070a3bd6eaa90685590158019d35c16092d301b80cb1/data diff --git a/modules/nf-core/multiqcsav/tests/main.nf.test.snap b/modules/nf-core/multiqcsav/tests/main.nf.test.snap index f0a8f3f4..603248d1 100644 --- a/modules/nf-core/multiqcsav/tests/main.nf.test.snap +++ b/modules/nf-core/multiqcsav/tests/main.nf.test.snap @@ -120,7 +120,7 @@ [ "MULTIQCSAV", "multiqc", - "1.34" + "1.35" ] ], "versions_interop": [ @@ -180,7 +180,7 @@ [ "MULTIQCSAV", "multiqc", - "1.34" + "1.35" ] ], "versions_interop": [ diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf deleted file mode 100644 index 17a2736c..00000000 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ /dev/null @@ -1,68 +0,0 @@ -process PICARD_COLLECTHSMETRICS { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "bait/*"), path(target_intervals, stageAs: "target/*") ,path(fasta) ,path(fai) ,path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - - def bait_interval_list = bait_intervals - def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/) { - bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - - def target_interval_list = target_intervals - def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/) { - target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - """ - export TMP=\$PWD - ${bait_intervallist_cmd} - ${target_intervallist_cmd} - - picard \\ - -Xmx${avail_mem}M \\ - CollectHsMetrics \\ - ${args} \\ - ${reference} \\ - --BAIT_INTERVALS ${bait_interval_list} \\ - --TARGET_INTERVALS ${target_interval_list} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics \\ - --TMP_DIR . - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectHsMetrics.coverage_metrics - """ -} diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml deleted file mode 100644 index 89bc502c..00000000 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ /dev/null @@ -1,129 +0,0 @@ -name: picard_collecthsmetrics -description: Collects hybrid-selection (HS) metrics for a SAM or BAM file. -keywords: - - alignment - - metrics - - statistics - - insert - - hybrid-selection - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - tool_dev_url: https://github.com/broadinstitute/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An aligned BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: [] - - bai: - type: file - description: Optional aligned BAM/CRAM/SAM file index - pattern: "*.{bai,crai,sai}" - ontologies: [] - - bait_intervals: - type: file - description: An interval file that contains the locations of the baits used. - pattern: "*.{interval_list,bed,bed.gz}" - ontologies: [] - - target_intervals: - type: file - description: An interval file that contains the locations of the targets. - pattern: "*.{interval_list,bed,bed.gz}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref: - type: file - description: | - A reference file to calculate dropout metrics measuring reduced representation of reads. - Optional input. - pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_fai: - type: file - description: Index of reference file. Only needed when reference is supplied. - pattern: "*.fai" - ontologies: [] - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_dict: - type: file - description: Sequence dictionary of FASTA file. Only needed when bed interval - lists are supplied. - pattern: "*.dict" - ontologies: [] - - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_gzi: - type: file - description: Index of reference file. Only needed when gzipped reference is supplied. - pattern: "*.gzi" - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -authors: - - "@projectoriented" - - "@matthdsm" -maintainers: - - "@projectoriented" - - "@matthdsm" diff --git a/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff b/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff deleted file mode 100644 index f9b0281a..00000000 --- a/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff +++ /dev/null @@ -1,62 +0,0 @@ -Changes in component 'nf-core/picard/collecthsmetrics' -'modules/nf-core/picard/collecthsmetrics/environment.yml' is unchanged -'modules/nf-core/picard/collecthsmetrics/meta.yml' is unchanged -Changes in 'picard/collecthsmetrics/main.nf': ---- modules/nf-core/picard/collecthsmetrics/main.nf -+++ modules/nf-core/picard/collecthsmetrics/main.nf -@@ -8,11 +8,7 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') -- tuple val(meta2), path(ref) -- tuple val(meta3), path(ref_fai) -- tuple val(meta4), path(ref_dict) -- tuple val(meta5), path(ref_gzi) -+ tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "bait/*"), path(target_intervals, stageAs: "target/*") ,path(fasta) ,path(fai) ,path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -24,7 +20,7 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -- def reference = ref ? "--REFERENCE_SEQUENCE ${ref}" : "" -+ def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - - def avail_mem = 3072 - if (!task.memory) { -@@ -38,16 +34,17 @@ - def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/) { - bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") -- bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." -+ bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - - def target_interval_list = target_intervals - def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/) { - target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") -- target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." -+ target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - """ -+ export TMP=\$PWD - ${bait_intervallist_cmd} - ${target_intervallist_cmd} - -@@ -59,7 +56,8 @@ - --BAIT_INTERVALS ${bait_interval_list} \\ - --TARGET_INTERVALS ${target_interval_list} \\ - --INPUT ${bam} \\ -- --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics -+ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics \\ -+ --TMP_DIR . - """ - - stub: - -'modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collecthsmetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test deleted file mode 100644 index d7366111..00000000 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ /dev/null @@ -1,221 +0,0 @@ -nextflow_process { - - name "Test Process PICARD_COLLECTHSMETRICS" - script "../main.nf" - process "PICARD_COLLECTHSMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collecthsmetrics" - - test("sarscov2 - bam") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - gzippedfa") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.gzi', checkIfExists: true)] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("sarscov2 - bam - nofasta") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[:],[]] - input[2] = [[:],[]] - input[3] = [[:],[]] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - bed") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - samebed") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true) - ] - - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } -} diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap deleted file mode 100644 index 43385314..00000000 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,639 +0,0 @@ -{ - "sarscov2 - bam - nofasta": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3548, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - "37\t0\t0", - "38\t0\t0", - "39\t0\t0", - "40\t0\t0", - "41\t0\t0", - "42\t0\t0", - "43\t0\t0", - "44\t0\t0", - "45\t0\t0", - "46\t0\t0", - "47\t0\t0", - "48\t0\t0", - "49\t0\t0", - "50\t0\t0", - "51\t0\t0", - "52\t0\t0", - "53\t0\t0", - "54\t0\t0", - "55\t0\t0", - "56\t0\t0", - "57\t0\t0", - "58\t0\t0", - "59\t0\t0", - "60\t0\t0", - "61\t0\t0", - "62\t0\t0", - "63\t0\t0", - "64\t0\t0", - "65\t0\t0", - "66\t0\t0", - "67\t0\t0", - "68\t0\t0", - "69\t0\t0", - "70\t0\t0", - "71\t0\t0", - "72\t0\t0", - "73\t0\t0", - "74\t0\t0", - "75\t0\t0", - "76\t0\t0", - "77\t0\t0", - "78\t0\t0", - "79\t0\t0", - "80\t0\t0", - "81\t0\t0", - "82\t0\t0", - "83\t0\t0", - "84\t0\t0", - "85\t0\t0", - "86\t0\t0", - "87\t0\t0", - "88\t0\t0", - "89\t0\t0" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-01-05T17:03:29.566021877", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "sarscov2 - bam - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-19T17:36:03.822502867", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "sarscov2 - bam - gzippedfa": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3601, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta.gz --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - "37\t0\t0", - "38\t0\t0", - "39\t0\t0", - "40\t0\t0", - "41\t0\t0", - "42\t0\t0", - "43\t0\t0", - "44\t0\t0", - "45\t0\t0", - "46\t0\t0", - "47\t0\t0", - "48\t0\t0", - "49\t0\t0", - "50\t0\t0", - "51\t0\t0", - "52\t0\t0", - "53\t0\t0", - "54\t0\t0", - "55\t0\t0", - "56\t0\t0", - "57\t0\t0", - "58\t0\t0", - "59\t0\t0", - "60\t0\t0", - "61\t0\t0", - "62\t0\t0", - "63\t0\t0", - "64\t0\t0", - "65\t0\t0", - "66\t0\t0", - "67\t0\t0", - "68\t0\t0", - "69\t0\t0", - "70\t0\t0", - "71\t0\t0", - "72\t0\t0", - "73\t0\t0", - "74\t0\t0", - "75\t0\t0", - "76\t0\t0", - "77\t0\t0", - "78\t0\t0", - "79\t0\t0", - "80\t0\t0", - "81\t0\t0", - "82\t0\t0", - "83\t0\t0", - "84\t0\t0", - "85\t0\t0", - "86\t0\t0", - "87\t0\t0", - "88\t0\t0", - "89\t0\t0" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-01-05T17:03:04.382110367", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "sarscov2 - bam - samebed": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3586, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t0\t0", - "1\t0\t0", - "2\t93\t0", - "3\t65\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t28", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t9", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t20", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t90", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t262", - 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3598, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - 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"test.CollectHsMetrics.coverage_metrics", - 3595, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - 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- conda-forge - - bioconda -dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf deleted file mode 100644 index e470007d..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ /dev/null @@ -1,60 +0,0 @@ -process PICARD_COLLECTMULTIPLEMETRICS { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta) , path(bam), path(bai), path(intervals), path(fasta) ,path(fai), path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val(meta), path("*.pdf"), emit: pdf, optional: true - tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def intervals_cmd = intervals ? "--INTERVALS ${intervals.join(',')}" : "" - def reference_cmd = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ - export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectMultipleMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectMultipleMetrics \\ - --TMP_DIR . \\ - ${reference_cmd} \\ - ${intervals_cmd} - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics - touch ${prefix}.CollectMultipleMetrics.insert_size_metrics - touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf - touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics - touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics - touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf - touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf - touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf - touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf - touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - """ -} diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml deleted file mode 100644 index 213d600b..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ /dev/null @@ -1,103 +0,0 @@ -name: picard_collectmultiplemetrics -description: Collect multiple metrics from a BAM file -keywords: - - alignment - - metrics - - statistics - - insert - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: SAM/BAM/CRAM file - pattern: "*.{sam,bam,cram}" - ontologies: [] - - bai: - type: file - description: Optional SAM/BAM/CRAM file index - pattern: "*.{sai,bai,crai}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta file - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - pdf: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.pdf": - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -authors: - - "@drpatelh" -maintainers: - - "@drpatelh" diff --git a/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff b/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff deleted file mode 100644 index 780c0862..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff +++ /dev/null @@ -1,49 +0,0 @@ -Changes in component 'nf-core/picard/collectmultiplemetrics' -'modules/nf-core/picard/collectmultiplemetrics/environment.yml' is unchanged -'modules/nf-core/picard/collectmultiplemetrics/meta.yml' is unchanged -Changes in 'picard/collectmultiplemetrics/main.nf': ---- modules/nf-core/picard/collectmultiplemetrics/main.nf -+++ modules/nf-core/picard/collectmultiplemetrics/main.nf -@@ -8,9 +8,7 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai) -- tuple val(meta2), path(fasta) -- tuple val(meta3), path(fai) -+ tuple val(meta) , path(bam), path(bai), path(intervals), path(fasta) ,path(fai), path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -23,7 +21,8 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -- def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" -+ def intervals_cmd = intervals ? "--INTERVALS ${intervals.join(',')}" : "" -+ def reference_cmd = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') -@@ -32,13 +31,16 @@ - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ -+ export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectMultipleMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectMultipleMetrics \\ -- ${reference} -+ --TMP_DIR . \\ -+ ${reference_cmd} \\ -+ ${intervals_cmd} - """ - - stub: - -'modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test deleted file mode 100644 index 0037acab..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ /dev/null @@ -1,186 +0,0 @@ - -nextflow_process { - - name "Test Process PICARD_COLLECTMULTIPLEMETRICS" - script "../main.nf" - process "PICARD_COLLECTMULTIPLEMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collectmultiplemetrics" - - test("test-picard-collectmultiplemetrics") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics-nofasta") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics-cram") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectmultiplemetrics-nofasta - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectmultiplemetrics-cram - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } -} diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap deleted file mode 100644 index 393ed100..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,242 +0,0 @@ -{ - "test-picard-collectmultiplemetrics": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:22:21.230301646", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:38.701455244", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectmultiplemetrics-nofasta - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:48.923918624", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectmultiplemetrics-cram": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:23:52.23446844", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics-nofasta": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:23:27.387621193", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics-cram - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:57.11686549", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml deleted file mode 100644 index 186d4a4b..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 - - conda-forge::r-base=4.4.1 diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf deleted file mode 100644 index 538f77be..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ /dev/null @@ -1,51 +0,0 @@ -process PICARD_COLLECTWGSMETRICS { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta), path(bam), path(bai) ,path(fasta) ,path(fai), path(dict) - path intervallist - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3072 - def interval = intervallist ? "--INTERVALS ${intervallist}" : '' - if (!task.memory) { - log.info('[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ - export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectWgsMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ - --REFERENCE_SEQUENCE ${fasta} \\ - --TMP_DIR . \\ - ${interval} - - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectWgsMetrics.coverage_metrics - """ -} diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml deleted file mode 100644 index c5afe2e7..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ /dev/null @@ -1,102 +0,0 @@ -name: picard_collectwgsmetrics -description: Collect metrics about coverage and performance of whole genome sequencing - (WGS) experiments. -keywords: - - alignment - - metrics - - statistics - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned reads file - pattern: "*.{bam, cram}" - ontologies: [] - - bai: - type: file - description: (Optional) Aligned reads file index - pattern: "*.{bai,crai}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta,fna}" - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome fasta file index - pattern: "*.{fai}" - ontologies: [] - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be generated - from a BED file with GATK BedToIntervalList. - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -authors: - - "@drpatelh" - - "@flowuenne" - - "@lassefolkersen" - - "@ramprasadn" -maintainers: - - "@drpatelh" - - "@flowuenne" - - "@lassefolkersen" - - "@ramprasadn" diff --git a/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff b/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff deleted file mode 100644 index 5de262d0..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff +++ /dev/null @@ -1,41 +0,0 @@ -Changes in component 'nf-core/picard/collectwgsmetrics' -'modules/nf-core/picard/collectwgsmetrics/environment.yml' is unchanged -'modules/nf-core/picard/collectwgsmetrics/meta.yml' is unchanged -Changes in 'picard/collectwgsmetrics/main.nf': ---- modules/nf-core/picard/collectwgsmetrics/main.nf -+++ modules/nf-core/picard/collectwgsmetrics/main.nf -@@ -8,10 +8,8 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai) -- tuple val(meta2), path(fasta) -- tuple val(meta3), path(fai) -- path intervallist -+ tuple val(meta), path(bam), path(bai) ,path(fasta) ,path(fai), path(dict) -+ path intervallist - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -32,6 +30,7 @@ - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ -+ export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectWgsMetrics \\ -@@ -39,7 +38,9 @@ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ - --REFERENCE_SEQUENCE ${fasta} \\ -+ --TMP_DIR . \\ - ${interval} -+ - """ - - stub: - -'modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test deleted file mode 100644 index 1bda5980..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ /dev/null @@ -1,138 +0,0 @@ - -nextflow_process { - - name "Test Process PICARD_COLLECTWGSMETRICS" - script "../main.nf" - process "PICARD_COLLECTWGSMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collectwgsmetrics" - - test("test-picard-collectwgsmetrics") { - - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectwgsmetrics-with-interval") { - - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectwgsmetrics - stub") { - options "-stub" - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectwgsmetrics-with-interval - stub") { - options "-stub" - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } -} diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap deleted file mode 100644 index 79f1145f..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,94 +0,0 @@ -{ - "test-picard-collectwgsmetrics-with-interval - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:35:04.636691319", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics-with-interval": { - "content": [ - false, - { - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:45.059411647", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:54.347278951", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics": { - "content": [ - false, - { - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:25.744978033", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/riker/multi/environment.yml similarity index 68% rename from modules/nf-core/picard/collecthsmetrics/environment.yml rename to modules/nf-core/riker/multi/environment.yml index b4ac4fe0..31a43156 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/riker/multi/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 + - bioconda::riker=0.2.0 diff --git a/modules/nf-core/riker/multi/main.nf b/modules/nf-core/riker/multi/main.nf new file mode 100644 index 00000000..0c70c3e7 --- /dev/null +++ b/modules/nf-core/riker/multi/main.nf @@ -0,0 +1,61 @@ +process RIKER_MULTI { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b1fa220679fac2077935260a88165214d8625b813ecb39cf129aecfba982c65/data' : + 'community.wave.seqera.io/library/riker:0.2.0--aa377939e8395424' }" + + input: + tuple val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai) + + output: + tuple val(meta), path("*.{txt,pdf}"), emit: metrics + tuple val("${task.process}"), val('riker'), eval("riker --version 2>&1 | sed 's/riker //'") , topic: versions, emit: versions_riker + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def ref = fasta ? "-r ${fasta}" : '' + def hybcap_opts = roi ? "--hybcap::baits ${roi} --hybcap::targets ${roi}" : '' + """ + riker multi \\ + -i ${bam} \\ + ${ref} \\ + -o ${prefix} \\ + --threads ${task.cpus} \\ + ${hybcap_opts} \\ + ${args} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.alignment-metrics.txt + touch ${prefix}.base-distribution-by-cycle.txt + touch ${prefix}.mean-quality-by-cycle.txt + touch ${prefix}.quality-score-distribution.txt + touch ${prefix}.error-mismatch.txt + touch ${prefix}.error-overlap.txt + touch ${prefix}.error-indel.txt + touch ${prefix}.gcbias-detail.txt + touch ${prefix}.gcbias-summary.txt + touch ${prefix}.hybcap-metrics.txt + touch ${prefix}.hybcap-per-target.txt + touch ${prefix}.hybcap-per-base.txt + touch ${prefix}.isize-metrics.txt + touch ${prefix}.isize-histogram.txt + touch ${prefix}.wgs-metrics.txt + touch ${prefix}.wgs-coverage.txt + touch ${prefix}.base-distribution-by-cycle.pdf + touch ${prefix}.gcbias-chart.pdf + touch ${prefix}.isize-histogram.pdf + touch ${prefix}.mean-quality-by-cycle.pdf + touch ${prefix}.quality-score-distribution.pdf + touch ${prefix}.wgs-coverage.pdf + """ +} diff --git a/modules/nf-core/riker/multi/meta.yml b/modules/nf-core/riker/multi/meta.yml new file mode 100644 index 00000000..93066a98 --- /dev/null +++ b/modules/nf-core/riker/multi/meta.yml @@ -0,0 +1,267 @@ +name: riker_multi +description: | + Run multiple riker collectors in a single BAM pass using riker multi. Specify + tools via ext.args (e.g. '--tools alignment basic isize'). The wgs and gcbias + tools require a reference FASTA; the hybcap tool requires baits and targets. +keywords: + - bam + - qc + - metrics + - multi + - alignment + - insert size + - gc bias + - coverage +tools: + - riker: + description: | + Fast Rust CLI toolkit for sequencing QC metrics. Ports key QC metrics tools + from Picard with cleaner output and better performance. + homepage: https://github.com/fulcrumgenomics/riker + documentation: https://github.com/fulcrumgenomics/riker + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned reads in BAM, CRAM, or SAM format + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_2572" # BAM + - edam: "http://edamontology.org/format_3462" # CRAM + - bai: + type: file + description: Index for the BAM/CRAM file + pattern: "*.{bai,crai}" + ontologies: + - edam: "http://edamontology.org/format_3327" # BAI + - baits: + type: file + description: Bait interval file (IntervalList or BED). Required when running the hybcap tool. Optional otherwise. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - targets: + type: file + description: Target interval file (IntervalList or BED). Required when running the hybcap tool. Optional otherwise. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file. Required when running wgs, gcbias, or error tools. + pattern: "*.{fa,fasta,fna}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA + - fai: + type: file + description: Index for the reference FASTA file + pattern: "*.fai" + ontologies: + - edam: "http://edamontology.org/format_3326" # FASTA index +output: + alignment_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.alignment-metrics.txt": + type: file + description: Alignment summary metrics (alignment tool) + pattern: "*.alignment-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + base_dist: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.base-distribution-by-cycle.txt": + type: file + description: Base distribution by cycle (basic tool) + pattern: "*.base-distribution-by-cycle.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + mean_qual: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.mean-quality-by-cycle.txt": + type: file + description: Mean quality by cycle (basic tool) + pattern: "*.mean-quality-by-cycle.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + qual_dist: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.quality-score-distribution.txt": + type: file + description: Quality score distribution (basic tool) + pattern: "*.quality-score-distribution.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_mismatch: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-mismatch.txt": + type: file + description: Base mismatch error metrics (error tool) + pattern: "*.error-mismatch.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_overlap: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-overlap.txt": + type: file + description: Read overlap error metrics (error tool) + pattern: "*.error-overlap.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_indel: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-indel.txt": + type: file + description: Indel error metrics (error tool) + pattern: "*.error-indel.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + gcbias_detail: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.gcbias-detail.txt": + type: file + description: Per-GC-bin detail metrics (gcbias tool) + pattern: "*.gcbias-detail.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + gcbias_summary: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.gcbias-summary.txt": + type: file + description: GC bias summary metrics (gcbias tool) + pattern: "*.gcbias-summary.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-metrics.txt": + type: file + description: Hybrid capture summary metrics (hybcap tool) + pattern: "*.hybcap-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_per_target: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-per-target.txt": + type: file + description: Per-target coverage metrics (hybcap tool, optional) + pattern: "*.hybcap-per-target.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_per_base: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-per-base.txt*": + type: file + description: Per-base coverage values (hybcap tool, optional) + pattern: "*.hybcap-per-base.txt{,.gz}" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + isize_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.isize-metrics.txt": + type: file + description: Insert size summary metrics (isize tool) + pattern: "*.isize-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + isize_histogram: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.isize-histogram.txt": + type: file + description: Insert size histogram (isize tool) + pattern: "*.isize-histogram.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + wgs_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.wgs-metrics.txt": + type: file + description: Whole-genome coverage summary metrics (wgs tool) + pattern: "*.wgs-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + wgs_coverage: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.wgs-coverage.txt": + type: file + description: Per-depth coverage histogram (wgs tool) + pattern: "*.wgs-coverage.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + pdf: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.pdf": + type: file + description: PDF plots from any tool that generates them + pattern: "*.pdf" + ontologies: + - edam: "http://edamontology.org/format_3508" # PDF + versions_riker: + - - ${task.process}: + type: string + description: The name of the process + - riker: + type: string + description: The name of the tool + - riker --version 2>&1 | sed 's/riker //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - riker: + type: string + description: The name of the tool + - riker --version 2>&1 | sed 's/riker //': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@emmcauley" +maintainers: + - "@emmcauley" diff --git a/modules/nf-core/riker/multi/riker-multi.diff b/modules/nf-core/riker/multi/riker-multi.diff new file mode 100644 index 00000000..11a621df --- /dev/null +++ b/modules/nf-core/riker/multi/riker-multi.diff @@ -0,0 +1,53 @@ +Changes in component 'nf-core/riker/multi' +'modules/nf-core/riker/multi/environment.yml' is unchanged +'modules/nf-core/riker/multi/meta.yml' is unchanged +Changes in 'riker/multi/main.nf': +--- modules/nf-core/riker/multi/main.nf ++++ modules/nf-core/riker/multi/main.nf +@@ -8,27 +8,10 @@ + 'community.wave.seqera.io/library/riker:0.2.0--aa377939e8395424' }" + + input: +- tuple val(meta), path(bam), path(bai), path(baits), path(targets) +- tuple val(meta2), path(fasta), path(fai) ++ tuple val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai) + + output: +- tuple val(meta), path("*.alignment-metrics.txt") , optional: true, emit: alignment_metrics +- tuple val(meta), path("*.base-distribution-by-cycle.txt") , optional: true, emit: base_dist +- tuple val(meta), path("*.mean-quality-by-cycle.txt") , optional: true, emit: mean_qual +- tuple val(meta), path("*.quality-score-distribution.txt") , optional: true, emit: qual_dist +- tuple val(meta), path("*.error-mismatch.txt") , optional: true, emit: error_mismatch +- tuple val(meta), path("*.error-overlap.txt") , optional: true, emit: error_overlap +- tuple val(meta), path("*.error-indel.txt") , optional: true, emit: error_indel +- tuple val(meta), path("*.gcbias-detail.txt") , optional: true, emit: gcbias_detail +- tuple val(meta), path("*.gcbias-summary.txt") , optional: true, emit: gcbias_summary +- tuple val(meta), path("*.hybcap-metrics.txt") , optional: true, emit: hybcap_metrics +- tuple val(meta), path("*.hybcap-per-target.txt") , optional: true, emit: hybcap_per_target +- tuple val(meta), path("*.hybcap-per-base.txt*") , optional: true, emit: hybcap_per_base +- tuple val(meta), path("*.isize-metrics.txt") , optional: true, emit: isize_metrics +- tuple val(meta), path("*.isize-histogram.txt") , optional: true, emit: isize_histogram +- tuple val(meta), path("*.wgs-metrics.txt") , optional: true, emit: wgs_metrics +- tuple val(meta), path("*.wgs-coverage.txt") , optional: true, emit: wgs_coverage +- tuple val(meta), path("*.pdf") , optional: true, emit: pdf ++ tuple val(meta), path("*.{txt,pdf}"), emit: metrics + tuple val("${task.process}"), val('riker'), eval("riker --version 2>&1 | sed 's/riker //'") , topic: versions, emit: versions_riker + + when: +@@ -38,10 +21,7 @@ + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def ref = fasta ? "-r ${fasta}" : '' +- if ((baits as Boolean) ^ (targets as Boolean)) { +- error "RIKER_MULTI: both 'baits' and 'targets' must be provided together, or neither" +- } +- def hybcap_opts = (baits && targets) ? "--hybcap::baits ${baits} --hybcap::targets ${targets}" : '' ++ def hybcap_opts = roi ? "--hybcap::baits ${roi} --hybcap::targets ${roi}" : '' + """ + riker multi \\ + -i ${bam} \\ + +'modules/nf-core/riker/multi/tests/main.nf.test.snap' is unchanged +'modules/nf-core/riker/multi/tests/nextflow.config' is unchanged +'modules/nf-core/riker/multi/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/riker/multi/tests/main.nf.test b/modules/nf-core/riker/multi/tests/main.nf.test new file mode 100644 index 00000000..616c9db3 --- /dev/null +++ b/modules/nf-core/riker/multi/tests/main.nf.test @@ -0,0 +1,344 @@ +nextflow_process { + + name "Test Process RIKER_MULTI" + script "../main.nf" + process "RIKER_MULTI" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "riker" + tag "riker/multi" + + test("sarscov2 - paired_end - bam - alignment basic isize") { + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - wgs gcbias") { + + when { + params { + module_args = '--tools wgs gcbias' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - wgs gcbias alignment basic isize") { + + when { + params { + module_args = '--tools wgs gcbias alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("homo_sapiens - paired_end - cram - alignment basic isize") { + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - hybcap") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - error") { + + when { + params { + module_args = '--tools error --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - error alignment") { + + when { + params { + module_args = '--tools error alignment --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - all tools") { + + when { + params { + module_args = '--tools alignment basic isize wgs gcbias hybcap error --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - baits without targets fails") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + [] + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assert process.failed + } + } + + test("sarscov2 - paired_end - bam - targets without baits fails") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assert process.failed + } + } + + test("sarscov2 - paired_end - bam - stub") { + + options "-stub" + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: 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], + "error_indel": [ + + ], + "error_mismatch": [ + + ], + "error_overlap": [ + + ], + "gcbias_detail": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gcbias-detail.txt:md5,44cd58d1a0bd81ca8ea5d3fa7c07e4db" + ] + ], + "gcbias_summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gcbias-summary.txt:md5,dd6d6d34bd4bdfdd815c452a68efa0e0" + ] + ], + "hybcap_metrics": [ + + ], + "hybcap_per_base": [ + + ], + "hybcap_per_target": [ + + ], + "isize_histogram": [ + + ], + "isize_metrics": [ + + ], + "mean_qual": [ + + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.gcbias-chart.pdf", + "test.wgs-coverage.pdf" + ] + ] + ], + "qual_dist": [ + + ], + "versions_riker": [ + [ + "RIKER_MULTI", + "riker", + "0.2.0" + ] + ], + "wgs_coverage": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wgs-coverage.txt:md5,8fd648b0045ff06fc3ba46772e33255c" + ] + ], + "wgs_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wgs-metrics.txt:md5,d7bb5636d4abeefe85f5ca2a6674adb2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-06-04T11:39:40.228372" + } +} \ No newline at end of file diff --git a/modules/nf-core/riker/multi/tests/nextflow.config b/modules/nf-core/riker/multi/tests/nextflow.config new file mode 100644 index 00000000..83152a66 --- /dev/null +++ b/modules/nf-core/riker/multi/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'RIKER_MULTI' { + ext.args = params.module_args + } +} diff --git a/nextflow.config b/nextflow.config index 20e156f9..5b2dff0c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -34,14 +34,15 @@ profiles { nextflow.enable.configProcessNamesValidation = true } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + appleContainer.enabled = false + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false + docker.enabled = true + docker.runOptions = '-u $(id -u):$(id -g)' + podman.enabled = false + shifter.enabled = false + singularity.enabled = false } arm64 { process.arch = 'arm64' @@ -54,62 +55,78 @@ profiles { wave.freeze = true wave.strategy = ["conda", "container"] } + apple { + appleContainer.enabled = true + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false + } emulate_amd64 { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + appleContainer.runOptions = '-u $(id -u):$(id -g) --arch amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true + appleContainer.enabled = false + apptainer.enabled = false + charliecloud.enabled = false conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.autoMounts = true + singularity.enabled = true } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + appleContainer.enabled = false + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false + docker.enabled = false + podman.enabled = true + shifter.enabled = false + singularity.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + appleContainer.enabled = false + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = true + singularity.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + appleContainer.enabled = false + apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + appleContainer.enabled = false + apptainer.autoMounts = true + apptainer.enabled = true + charliecloud.enabled = false + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false } wave { - apptainer.ociAutoPull = true - singularity.ociAutoPull = true - wave.enabled = true - wave.freeze = true wave.strategy = ["conda", "container"] + wave.freeze = true + wave.enabled = true + singularity.ociAutoPull = true + apptainer.ociAutoPull = true } gpu { docker.runOptions = '-u $(id -u):$(id -g) --gpus all' diff --git a/subworkflows/local/bam_qc/main.nf b/subworkflows/local/bam_qc/main.nf index fb2452b2..e38493d4 100644 --- a/subworkflows/local/bam_qc/main.nf +++ b/subworkflows/local/bam_qc/main.nf @@ -1,64 +1,35 @@ // samtools modules -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' -// picard modules -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' -include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' -include { PICARD_COLLECTWGSMETRICS } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +// riker modules +include { RIKER_MULTI } from '../../../modules/nf-core/riker/multi/main' workflow BAM_QC { take: - ch_bam_bai_roi_fasta_fai_dict // channel: [ val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai), path(dict)] + ch_bam_bai_roi_fasta_fai // channel: [ val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai)] main: - ch_bam_bai_roi_fasta_fai_dict - .map { meta, bam, bai, _roi, fasta, fai, _dict -> + ch_bam_bai_roi_fasta_fai + .map { meta, bam, bai, _roi, fasta, fai -> return [meta, bam, bai, fasta, fai] } .set { ch_bam_bai_fasta_fai } SAMTOOLS_STATS(ch_bam_bai_fasta_fai) - SAMTOOLS_FLAGSTAT(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> return [meta, bam, bai] }) - SAMTOOLS_IDXSTATS(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> return [meta, bam, bai] }) + SAMTOOLS_FLAGSTAT(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> + return [meta, bam, bai] + }) + SAMTOOLS_IDXSTATS(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> + return [meta, bam, bai] + }) - ch_picard_hsmetrics = channel.empty() - ch_picard_multiplemetrics = channel.empty() - ch_picard_multiplemetrics_pdf = channel.empty() - ch_picard_wgsmetrics = channel.empty() - - ch_bam_bai_roi_fasta_fai_dict - .filter { meta, _bam, _bai, _roi, _fasta, _fai, _dict -> - !meta.disable_picard_metrics - } - .set { ch_picard } - - PICARD_COLLECTMULTIPLEMETRICS(ch_picard) - ch_picard_multiplemetrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - ch_picard_multiplemetrics_pdf = PICARD_COLLECTMULTIPLEMETRICS.out.pdf - - ch_picard - .branch { meta, bam, bai, roi, fasta, fai, dict -> - hsmetrics: roi != [] - return [meta, bam, bai, roi, roi, fasta, fai, dict] - wgsmetrics: roi == [] - return [meta, bam, bai, fasta, fai, dict] - } - .set { ch_picard_coverage } - - PICARD_COLLECTWGSMETRICS(ch_picard_coverage.wgsmetrics, []) - ch_picard_wgsmetrics = PICARD_COLLECTWGSMETRICS.out.metrics - - PICARD_COLLECTHSMETRICS(ch_picard_coverage.hsmetrics) - ch_picard_hsmetrics = PICARD_COLLECTHSMETRICS.out.metrics + RIKER_MULTI(ch_bam_bai_roi_fasta_fai) emit: - samtools_stats = SAMTOOLS_STATS.out.stats - samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat - samtools_idxstats = SAMTOOLS_IDXSTATS.out.idxstats - picard_multiplemetrics = ch_picard_multiplemetrics - picard_multiplemetrics_pdf = ch_picard_multiplemetrics_pdf - picard_wgsmetrics = ch_picard_wgsmetrics - picard_hsmetrics = ch_picard_hsmetrics + samtools_stats = SAMTOOLS_STATS.out.stats + samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat + samtools_idxstats = SAMTOOLS_IDXSTATS.out.idxstats + riker_metrics = RIKER_MULTI.out.metrics } diff --git a/tests/subworkflows/local/bam_qc/main.nf.test b/tests/subworkflows/local/bam_qc/main.nf.test index acb2f53a..c210d73f 100644 --- a/tests/subworkflows/local/bam_qc/main.nf.test +++ b/tests/subworkflows/local/bam_qc/main.nf.test @@ -13,15 +13,14 @@ nextflow_workflow { when { workflow { """ - // [meta, bam, bai, roi, fasta, fai, dict] + // [meta, bam, bai, roi, fasta, fai] input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:false ], + [ id:'test', single_end:false ], file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), ]) """ } @@ -30,12 +29,7 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) + sanitizeOutput(workflow.out, unstableKeys:[]) ).match() } @@ -45,46 +39,14 @@ nextflow_workflow { when { workflow { """ - // [meta, bam, bai, roi, fasta, fai, dict] + // [meta, bam, bai, roi, fasta, fai] input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:false ], + [ id:'test', single_end:false ], file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), [], file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), - ]) - """ - } - } - - then { - assert workflow.success - assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) - ).match() - } - } - - test("Bam QC - Samtools") { - when { - workflow { - """ - // [meta, bam, bai, roi, fasta, fai, dict] - input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:true ], - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), ]) """ } @@ -93,12 +55,7 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) + sanitizeOutput(workflow.out, unstableKeys:[]) ).match() } } diff --git a/tests/subworkflows/local/bam_qc/main.nf.test.snap b/tests/subworkflows/local/bam_qc/main.nf.test.snap index 0f1dea8d..ffa60858 100644 --- a/tests/subworkflows/local/bam_qc/main.nf.test.snap +++ b/tests/subworkflows/local/bam_qc/main.nf.test.snap @@ -2,110 +2,31 @@ "Bam QC - HSmetrics": { "content": [ { - "picard_hsmetrics": [ + "riker_metrics": [ [ { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics" - ] - ], - "picard_multiplemetrics": [ - [ - { - "disable_picard_metrics": false, "id": "test", "single_end": false }, [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" + "test.alignment-metrics.txt:md5,6afbb56c56893875c8e580704f9553fb", + "test.base-distribution-by-cycle.pdf:md5,43dcb037a557e5cbf784f340cadc02e1", + "test.base-distribution-by-cycle.txt:md5,a1554060830f234d63a282c89fa47b2a", + "test.isize-histogram.pdf:md5,c18e427f1c7e4c8f164557da30ad9d71", + "test.isize-histogram.txt:md5,377a5662dd0bd893e2fb9bcec50ccd81", + "test.isize-metrics.txt:md5,77611ea453436da4af1619283d8d1a7b", + "test.mean-quality-by-cycle.pdf:md5,e5ab33ce654788037f4d6f2b41038001", + "test.mean-quality-by-cycle.txt:md5,2f257f4133b678c7c953cb30714548d6", + "test.quality-score-distribution.pdf:md5,fd61e5e131a0b71d225decc167b29101", + "test.quality-score-distribution.txt:md5,0187a3f6c5bace7415a19e510c9d7ddc" ] ] - ], - "picard_multiplemetrics_pdf": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ] - ] - ], - "picard_wgsmetrics": [ - ], "samtools_flagstat": [ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" - ] - ], - "samtools_idxstats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" - ] - ], - "samtools_stats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.stats:md5,ff81063faa5cf509f16044c4160733b5" - ] - ] - } - ], - "timestamp": "2026-03-25T18:43:20.761133", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - } - }, - "Bam QC - Samtools": { - "content": [ - { - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ - - ], - "picard_multiplemetrics_pdf": [ - - ], - "picard_wgsmetrics": [ - - ], - "samtools_flagstat": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": true + "single_end": false }, "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" ] @@ -114,8 +35,7 @@ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": true + "single_end": false }, "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" ] @@ -124,74 +44,47 @@ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": true + "single_end": false }, "test.stats:md5,ff81063faa5cf509f16044c4160733b5" ] ] } ], - "timestamp": "2026-03-25T18:44:55.125939", + "timestamp": "2026-06-15T07:38:49.8639", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "Bam QC - WGSmetrics": { "content": [ { - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ + "riker_metrics": [ [ { - "disable_picard_metrics": false, "id": "test", "single_end": false }, [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" + "test.alignment-metrics.txt:md5,6afbb56c56893875c8e580704f9553fb", + "test.base-distribution-by-cycle.pdf:md5,71ccfb355fc2fa585ecab03a3487a63b", + "test.base-distribution-by-cycle.txt:md5,a1554060830f234d63a282c89fa47b2a", + "test.isize-histogram.pdf:md5,c18e427f1c7e4c8f164557da30ad9d71", + "test.isize-histogram.txt:md5,377a5662dd0bd893e2fb9bcec50ccd81", + "test.isize-metrics.txt:md5,77611ea453436da4af1619283d8d1a7b", + "test.mean-quality-by-cycle.pdf:md5,4ebf87a4d12db4269267b56d0441388e", + "test.mean-quality-by-cycle.txt:md5,2f257f4133b678c7c953cb30714548d6", + "test.quality-score-distribution.pdf:md5,fd61e5e131a0b71d225decc167b29101", + "test.quality-score-distribution.txt:md5,0187a3f6c5bace7415a19e510c9d7ddc" ] ] ], - "picard_multiplemetrics_pdf": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ] - ] - ], - "picard_wgsmetrics": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics" - ] - ], "samtools_flagstat": [ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": false + "single_end": false }, "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" ] @@ -200,8 +93,7 @@ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": false + "single_end": false }, "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" ] @@ -210,18 +102,17 @@ [ { "id": "test", - "single_end": false, - "disable_picard_metrics": false + "single_end": false }, "test.stats:md5,ff81063faa5cf509f16044c4160733b5" ] ] } ], - "timestamp": "2026-03-25T18:44:25.625109", + "timestamp": "2026-06-15T07:40:29.049547", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/workflows/preprocessing.nf.test b/tests/workflows/preprocessing.nf.test index c2770b1a..874aec15 100644 --- a/tests/workflows/preprocessing.nf.test +++ b/tests/workflows/preprocessing.nf.test @@ -76,10 +76,6 @@ nextflow_workflow { "multiqcsav_data", "multiqcsav_plots", "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", "samtools_coverage", "samtools_flagstat", "samtools_stats" @@ -157,10 +153,6 @@ nextflow_workflow { "multiqcsav_data", "multiqcsav_plots", "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", "samtools_coverage", "samtools_flagstat", "samtools_stats" @@ -169,11 +161,9 @@ nextflow_workflow { } } - test("preprocessing - fastq - bwa - bamsormadup - roi - no coverage/no picard") { + test("preprocessing - fastq - bwa - bamsormadup - roi - no coverage") { when { params { - run_coverage = false - disable_picard_metrics = true } workflow { """ @@ -190,7 +180,6 @@ nextflow_workflow { aligner: "bwamem", markdup: "bamsormadup", run_coverage: false, - disable_picard_metrics: true, roi: "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed" ], //fastq_1 @@ -243,10 +232,6 @@ nextflow_workflow { "multiqcsav_data", "multiqcsav_plots", "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", "samtools_coverage", "samtools_flagstat", "samtools_stats" @@ -316,10 +301,6 @@ nextflow_workflow { "multiqcsav_data", "multiqcsav_plots", "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", "samtools_coverage", "samtools_flagstat", "samtools_stats" diff --git a/tests/workflows/preprocessing.nf.test.snap b/tests/workflows/preprocessing.nf.test.snap index 5338b7c2..29c6754d 100644 --- a/tests/workflows/preprocessing.nf.test.snap +++ b/tests/workflows/preprocessing.nf.test.snap @@ -459,105 +459,44 @@ "panelcoverage": [ ], - "picard_hsmetrics": [ + "riker_metrics": [ [ { "groupSize": 1, "groupTarget": { - "aligner": "bwamem", - "genome": "GRCh38", - "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1", + "samplename": "sample1", "library": "test", - "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "tag": "WES", "sample_type": "DNA", - "samplename": "sample1", - "single_end": false, - "tag": "WES" - } - }, - "sample1.CollectHsMetrics.coverage_metrics" - ] - ], - "picard_multiplemetrics": [ - [ - { - "groupSize": 1, - "groupTarget": { "aligner": "bwamem", - "genome": "GRCh38", - "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1", - "library": "test", "markdup": "bamsormadup", - "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "run_coverage": true, - "sample_type": "DNA", - "samplename": "sample1", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "single_end": false, - "tag": "WES" - } - }, - [ - "sample1.CollectMultipleMetrics.alignment_summary_metrics", - "sample1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "picard_multiplemetrics_pdf": [ - [ - { - "groupSize": 1, - "groupTarget": { - "aligner": "bwamem", "genome": "GRCh38", "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1", - "library": "test", - "markdup": "bamsormadup", - "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, - "sample_type": "DNA", - "samplename": "sample1", - "single_end": false, - "tag": "WES" + "id": "sample1" } }, [ - "sample1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_distribution.pdf", - "sample1.CollectMultipleMetrics.read_length_histogram.pdf" + "sample1.alignment-metrics.txt:md5,0c6f36de09941f6d379bed9e772e50c1", + "sample1.base-distribution-by-cycle.pdf:md5,0fbd0473740dc74751af4d4503511a5f", + "sample1.base-distribution-by-cycle.txt:md5,832a8f50ac2102d5ffc6d796bec099a3", + "sample1.isize-histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.isize-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.mean-quality-by-cycle.pdf:md5,f90eae685942493bdf1df90d39650c2c", + "sample1.mean-quality-by-cycle.txt:md5,022828223ec254dc82935ee886413fbe", + "sample1.quality-score-distribution.pdf:md5,0564c904cc1234189061a6f5362393f6", + "sample1.quality-score-distribution.txt:md5,89e46bfc59dbc7aed65d9c1e2350dd3a" ] ] - ], - "picard_wgsmetrics": [ - ], "rna_junctions": [ @@ -712,13 +651,13 @@ ] } ], - "timestamp": "2026-05-19T14:56:03.18527", + "timestamp": "2026-06-15T08:36:58.835655", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.3" } }, - "preprocessing - fastq - bwa - bamsormadup - roi - no coverage/no picard": { + "preprocessing - fastq - bwa - bamsormadup - no roi": { "content": [ { "align_reports": [ @@ -730,7 +669,6 @@ "groupSize": 1, "groupTarget": { "aligner": "bwamem", - "disable_picard_metrics": true, "genome": "GRCh38", "genome_data": { "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", @@ -743,12 +681,11 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": false, + "run_coverage": true, "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, "sample1.cram", @@ -775,7 +712,6 @@ { "aligner": "bwamem", "count": 1, - "disable_picard_metrics": true, "genome": "GRCh38", "genome_data": { "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", @@ -796,12 +732,11 @@ "PU": 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"single_end": false, + "tag": "WES" + }, + "sample1.fastp.html" + ] + ], + "fastp_json": [ + [ + { + "id": "sample1", + "samplename": "sample1", + "library": "test", + "organism": "Homo sapiens", + "tag": "WES", + "sample_type": "DNA", + "aligner": "bwamem", + "markdup": "bamsormadup", + "run_coverage": false, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "single_end": false, + "readgroup": { + "LB": "test", + "CN": "", + "PL": "ILLUMINA", + "SM": "sample1", + "ID": "H5T2YDSX3.1", + "PU": "H5T2YDSX3.1" + }, + "genome": "GRCh38", + "genome_data": { + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" + }, + "count": 1 + }, + "sample1.fastp.json:md5,759cb3337e9a02f54a9dcb7582288a60" + ] + ], + "fastq": [ + + ], + "md5sums": [ [ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WGS", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1" + "id": "sample1", + "library": "test", + "markdup": "bamsormadup", + "organism": "Homo sapiens", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "run_coverage": false, + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WES" } }, - "sample1.mosdepth.summary.txt:md5,699b955719b06ff290edbe0692492213" + "sample1.md5" ] + ], + "mosdepth_global": [ + + ], + "mosdepth_per_base_bed": [ + + ], + "mosdepth_per_base_csi": [ + + ], + "mosdepth_per_base_d4": [ + + ], + "mosdepth_quantized_bed": [ + + ], + "mosdepth_quantized_csi": [ + + ], + "mosdepth_regions": [ + + ], + "mosdepth_regions_bed": [ + + ], + "mosdepth_regions_csi": [ + + ], + "mosdepth_summary": [ + ], "mosdepth_thresholds_bed": [ @@ -1469,101 +1447,43 @@ "panelcoverage": [ ], - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ + "riker_metrics": [ [ { "groupSize": 1, "groupTarget": { - "aligner": "bwamem", - "genome": "GRCh38", - "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1", + "samplename": "sample1", "library": "test", - "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "tag": "WES", "sample_type": "DNA", - "samplename": "sample1", - "single_end": false, - "tag": "WGS" - } - }, - [ - "sample1.CollectMultipleMetrics.alignment_summary_metrics", - "sample1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "picard_multiplemetrics_pdf": [ - [ - { - "groupSize": 1, - "groupTarget": { "aligner": "bwamem", - "genome": "GRCh38", - "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1", - "library": "test", "markdup": "bamsormadup", - "organism": "Homo sapiens", - "run_coverage": true, - "sample_type": "DNA", - "samplename": "sample1", + "run_coverage": false, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "single_end": false, - "tag": "WGS" - } - }, - [ - "sample1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_distribution.pdf", - "sample1.CollectMultipleMetrics.read_length_histogram.pdf" - ] - ] - ], - "picard_wgsmetrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "aligner": "bwamem", "genome": "GRCh38", "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1", - "library": "test", - "markdup": "bamsormadup", - "organism": "Homo sapiens", - "run_coverage": true, - "sample_type": "DNA", - "samplename": "sample1", - "single_end": false, - "tag": "WGS" + "id": "sample1" } }, - "sample1.CollectWgsMetrics.coverage_metrics" + [ + "sample1.alignment-metrics.txt:md5,0c6f36de09941f6d379bed9e772e50c1", + "sample1.base-distribution-by-cycle.pdf:md5,0fbd0473740dc74751af4d4503511a5f", + "sample1.base-distribution-by-cycle.txt:md5,832a8f50ac2102d5ffc6d796bec099a3", + "sample1.isize-histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.isize-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.mean-quality-by-cycle.pdf:md5,f90eae685942493bdf1df90d39650c2c", + "sample1.mean-quality-by-cycle.txt:md5,022828223ec254dc82935ee886413fbe", + "sample1.quality-score-distribution.pdf:md5,0564c904cc1234189061a6f5362393f6", + "sample1.quality-score-distribution.txt:md5,89e46bfc59dbc7aed65d9c1e2350dd3a" + ] ] ], "rna_junctions": [ @@ -1573,32 +1493,7 @@ ], "samtools_coverage": [ - [ - { - "groupSize": 1, - "groupTarget": { - "aligner": "bwamem", - "genome": "GRCh38", - "genome_data": { - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1", - "library": "test", - "markdup": "bamsormadup", - "organism": "Homo sapiens", - "run_coverage": true, - "sample_type": "DNA", - "samplename": "sample1", - "single_end": false, - "tag": "WGS" - } - }, - "sample1.coverage.txt" - ] + ], "samtools_flagstat": [ [ @@ -1618,11 +1513,12 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "run_coverage": false, "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, "sample1.flagstat" @@ -1636,11 +1532,12 @@ "samplename": "sample1", "library": "test", "organism": "Homo sapiens", - "tag": "WGS", + "tag": "WES", "sample_type": "DNA", "aligner": "bwamem", "markdup": "bamsormadup", - "run_coverage": true, + "run_coverage": false, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "single_end": false, "genome": "GRCh38", "genome_data": { @@ -1674,11 +1571,12 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "run_coverage": false, "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, "sample1.stats" @@ -1692,11 +1590,12 @@ "samplename": "sample1", "library": "test", "organism": "Homo sapiens", - "tag": "WGS", + "tag": "WES", "sample_type": "DNA", "aligner": "bwamem", "markdup": "bamsormadup", - "run_coverage": true, + "run_coverage": false, + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "single_end": false, "genome": "GRCh38", "genome_data": { @@ -1714,10 +1613,10 @@ ] } ], - "timestamp": "2026-05-19T14:59:02.416267", + "timestamp": "2026-06-15T09:20:27.039822", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.3" } }, "preprocessing - flowcell - bwa - bamsormadup - roi": { @@ -1756,7 +1655,6 @@ "adapter_R1": null, "adapter_R2": null, "run_coverage": true, - "disable_picard_metrics": true, "roi": null, "genome_data": { "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", @@ -1773,10 +1671,10 @@ ] } ], - "timestamp": "2026-05-19T12:26:24.789934", + "timestamp": "2026-06-15T08:43:48.791593", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/workflows/preprocessing.nf b/workflows/preprocessing.nf index 46c93597..e7c5b9e4 100644 --- a/workflows/preprocessing.nf +++ b/workflows/preprocessing.nf @@ -316,7 +316,6 @@ workflow PREPROCESSING { meta.roi && meta.roi != [] ? file(meta.roi, checkIfExists: true) : [], getGenomeAttribute(meta.genome_data, "fasta"), getGenomeAttribute(meta.genome_data, "fai"), - getGenomeAttribute(meta.genome_data, "dict"), ] } .set { ch_bam_qc } @@ -326,10 +325,7 @@ workflow PREPROCESSING { BAM_QC.out.samtools_stats, BAM_QC.out.samtools_flagstat, BAM_QC.out.samtools_idxstats, - BAM_QC.out.picard_multiplemetrics, - BAM_QC.out.picard_wgsmetrics, - BAM_QC.out.picard_wgsmetrics, - BAM_QC.out.picard_hsmetrics, + BAM_QC.out.riker_metrics, ) /* @@ -449,10 +445,7 @@ workflow PREPROCESSING { samtools_stats = BAM_QC.out.samtools_stats samtools_flagstat = BAM_QC.out.samtools_flagstat samtools_idxstats = BAM_QC.out.samtools_idxstats - picard_multiplemetrics = BAM_QC.out.picard_multiplemetrics - picard_multiplemetrics_pdf = BAM_QC.out.picard_multiplemetrics_pdf - picard_wgsmetrics = BAM_QC.out.picard_wgsmetrics - picard_hsmetrics = BAM_QC.out.picard_hsmetrics + riker_metrics = BAM_QC.out.riker_metrics md5sums = MD5SUM.out.checksum multiqcsav_report = MULTIQCSAV.out.report.toList() multiqcsav_data = MULTIQCSAV.out.data.toList()