Add generate-SQC-BAM

[yashpatel6]

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• 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

[nwiltsie]

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?

[yashpatel6]

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

[nwiltsie]

Looks good to me!

[sorelfitzgibbon]

LGTM! A couple of minor comments.

[Faizal-Eeman]

Looks good. Two comments.