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Sfitz add fastqc and switch to process_afterscript for logs #60
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sorelfitzgibbon
commented
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_filename
to create an additional output directory with thedataset_id
and theid
extracted 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
FastQC
workflowNFTest
forFastQC
process_afterscript
including for publication of logs.Closes #45
Testing Results
output:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc
nftest a_mini-all-tools
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T214738Z.log
nftest a_mini-all-tools-multiple-samples
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T221709Z.log
nftest a_mini-fastqc
log:
/hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/unreleased/sfitz-add-fastqc/log-nftest-20240605T222627Z.log
Checklist
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
manifest
block in thenextflow.config
as 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.md
under the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yaml
andmanifest
block of thenextflow.config
file 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.