Sfitz concat vcf #213
Sfitz concat vcf #213
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Converting to a draft as I realized the output needs to be uncompressed for the next step and some checksums need to be added. |
| publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}", | ||
| mode: "copy", | ||
| pattern: "*concat.vcf", | ||
| enabled: params.save_intermediate_files |
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this intermediate file will be used by vcf2maf (and has to be uncompressed)
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One minor naming suggestion! Otherwise looks good to me!
Anything else @yashpatel6
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I haven't done any runs with large samples since adding plot_VennDiagram_R or concat_VCFs_BCFtools so these are just guesses. These two processes will run together, but only after everything is done. I doubt they use much memory so I don't think it matters much. The next PR, add maf, will add one more process and may be the last PR before release. With that I could test with large samples and look at memory as well as which processes will use more cpus.
module/intersect-processes.nf
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| publishDir path: "${params.workflow_output_dir}/output", | ||
| mode: "copy", | ||
| pattern: "isec-1-or-more/*.txt" |
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Any reason this was moved here from the intersect process? Generally, we want to publish files from the process that generated them
| @@ -78,4 +78,24 @@ process { | |||
| } | |||
| } | |||
| } | |||
| withName: plot_VennDiagram_R { | |||
| cpus = 2 | |||
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Can VennDiagram take 2 CPUs?
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As I sort of mentioned in the PR description, these are just placeholders until I do a large bam test run before the release. I will adjust these and the processes added in sfitz-add-maf at that time.
| } | ||
| } | ||
| withName: concat_VCFs_BCFtools { | ||
| cpus = 2 |
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It looks like this process doesn't use 2 CPUs?
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Looks good! The resources allocations can be tuned after running the large sample in a future PR. Anything else to add @tyamaguchi-ucla ?
Description
Add BCFtools process to concatenate the 2+ tool consensus variants into one VCF. The output header is a uniquified concatenation of all headers. The output fields:
INFOFORMATNORMALandTUMORare from the first listed VCF that has the variant.Testing Results
nftest run a_mini_n2-all-tools-std-input
log:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-concat-vcf/log-nftest-20230810T214722Z.logoutput:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-concat-vcf/a_mini_n2-all-tools-std-inputChecklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added my name to the contributors listings in the
manifestblock in thenextflow.configas part of this pull request; I am listed already, or do not wish to be listed. (This acknowledgement is optional.)I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)I have tested the pipeline on at least one A-mini sample.