Sfitz add fastqc and switch to process_afterscript for logs #60
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sorelfitzgibbon
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Jun 5, 2024
module/fastqc.nf
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| output_filename = generate_standard_filename("FastQC-${params.fastqc_version}", | ||
| params.dataset_id, | ||
| id, | ||
| [:]) | ||
|
|
||
| """ | ||
| set -euo pipefail | ||
| mkdir "${output_filename}" | ||
| fastqc \ | ||
| --outdir "${output_filename}" \ |
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- In this case I used
generate_standard_filenameto create an additional output directory with thedataset_idand theidextracted from the input BAM files. - An alternate possibility is to output to "./" and then rename the files within
${bam_prefix}_fastqc(i.e. the FastQC directory that is always created) to include the standard_filename components.
|
After discussion with @yashpatel6 I will look into methods to get output separated by read-group. |
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Description
FastQCworkflowNFTestforFastQCprocess_afterscriptincluding for publication of logs.Closes #45
Testing Results
output:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqcnftest a_mini-all-tools
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T214738Z.lognftest a_mini-all-tools-multiple-samples
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T221709Z.lognftest a_mini-fastqc
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T222627Z.logChecklist
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, am listedalready, 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 using NFTest, or I have justified why I did not need to run NFTest above.