nf-cmgg · matthdsm · Jun 5, 2026 · Jun 5, 2026 · Jun 8, 2026 · Jun 14, 2026
diff --git 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/)
 
 <picture>

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git 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
diff --git 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
 <summary>Output files</summary>
 
 - `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