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Add generate-SQC-BAM #174
Add generate-SQC-BAM #174
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It looks like there's some problem with the outputs in test-metapipeline-DNA-fastq-input.log
:
2024-03-16 03:49:21,820 - NFTest - INFO - WARN: Access to undefined parameter `input_csv` -- Initialise it to a default value eg. `params.input_csv = some_value`
2024-03-16 05:46:02,793 - NFTest - INFO - WARN: Failed to publish file: /scratch/107838/49/5d54845765959a8a2149b022e031da/generate-SQC-BAM-1.0.0/IlluminaPatient1; to: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-add-sqc-bam/test-metapipeline-DNA-fastq-input/metapipeline-DNA-6.0.0-rc.1/IlluminaTest/main_workflow/output/generate-SQC-BAM-1.0.0/IlluminaPatient1 [copy] -- See log file for details
2024-03-16 05:46:03,022 - NFTest - INFO - WARN: Failed to publish file: /scratch/107838/49/5d54845765959a8a2149b022e031da/generate-SQC-BAM-1.0.0/IlluminaPatient1; to: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-add-sqc-bam/test-metapipeline-DNA-fastq-input/metapipeline-DNA-6.0.0-rc.1/IlluminaTest/main_workflow/output/generate-SQC-BAM-1.0.0/IlluminaPatient1 [copy] -- See log file for details
I don't see those lines in test-metapipeline-DNA-batch.log
. Is the same directory getting copied three times and failing the last two, or are multiple samples getting aliased to the same place?
It was an issue with over-writing since the patient ID was being used as the identifier in single-sample mode; updated now to assign the ID based on run mode |
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Looks good to me!
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LGTM! A couple of minor comments.
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Looks good. Two comments.
Co-authored-by: Sorel Fitz-Gibbon <3223552+sorelfitzgibbon@users.noreply.github.com>
Co-authored-by: Sorel Fitz-Gibbon <3223552+sorelfitzgibbon@users.noreply.github.com>
I have read the code review guidelines and the code review best practice on GitHub check-list.
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
metadata.yaml
and themanifest
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 on at least one A-mini sample.
Adding generate-SQC-BAM pipeline, with SAMtools stats and Picard CollectWgsMetrics enabled by default.
Testing Results
Tested with NFTest:
test-generate-SQC-BAM
,test-metapipeline-DNA-batch
,test-metapipeline-DNA-fastq-input
- logs and output:/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-add-sqc-bam