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…t and schema_input
Added and integrated the samtools/view module, updated the sampleshee…
…samtools/sort module
Added position specifier for samtools/view, added and integrated the …
Added samtools/fastq module and integrated it
Added and integrated pear module
…eads and modified versions.yml
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Added a module to merge reads
Cmgg multiqc
Add connection to nf-cmgg configs
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Shouldn't this be reference data, or at least live somewhere else? (e.g. outside the pipeline)
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Good catch! I forgot to move it
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There is one input file per mini pipeline present in the pipeline, I kept it separate because the flows don't interact with eachother and this kept it more clear
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This is a bash script, port it to a module
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What is the holy hell is this even and why can't this be done with a "normal" tool and a module in multiiqc_cmgg ?
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It's a bit too complex for a multiqc, I tried, this would need a UI on its own which would take more work than we currently have time for
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Ditch this and use the config from nf-cmgg/configs or remove it entirely
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Drop custom module, use nf-core CAT_FASTQ or something
| fq_all = f"{outputdir}/{sample}_all.fastq.gz" | ||
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| ### extract reads from BAM/CRAM ### | ||
| subprocess.check_output(f"{samtools} view -T {reference_genome} {cram} {pos} -F 12 -b -o {bam}", stderr=subprocess.STDOUT, shell=True) |
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Are you kidding me....? pythonbash?
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🙂 This is the original script, now replaced by the targeted.nf workflow, and can be removed.
| ### check if file is not empty (otherwise pear goes in ERROR) ### | ||
| if os.path.getsize(fq_r1) != 0: | ||
| ### merge overlapping read pairs using pear ### | ||
| subprocess.check_output(f"{pear} --forward-fastq {fq_r1} --reverse-fastq {fq_r2} --output {fq_p} >> {log}", stderr=subprocess.STDOUT, shell=True) |
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Why do we run pear, or any other tool here when we have a module??
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This is the original script, now replaced by the targeted.nf workflow, and can be removed.
matthdsm
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matthdsm
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I don't really like adding all the crap to the history, but whatever I guess.
Let's just do this and then deprecate this pipeline ASAP entirely
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First release of the pipeline