Nzeltser format output dir

[alkaZeltser]

Description

Format output directories/files according to lab standards. Also testing a few combinations of input file sizes.

Testing Results

All run interactively on F2 node. Based on the trace files, peak_vmem doesn't scale much with file size, hovering below 11MB. Runtime is affected significantly by the size of the bedfile (not so much the BAM).

• Case 1: small BAM + small BED
  • sample: A-mini S2.T-n1
  • input yaml: /hot/user/nzeltser/pipeline-targeted-coverage/test/input/a-mini-n1.yaml
  • config: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-format-output-dir/small-bed/targeted-coverage-nf-1.0.0-rc.1/A-mini-n1/
• Case 2: real BAM + small BED
  • sample: BZPRGPT1000001-N001-B01-F (targeted sequencing sample from PRAD0000049)
  • input yaml: /hot/user/nzeltser/pipeline-targeted-coverage/test/input/BZPRGPT1000001-N001-B01-F.yaml
  • config: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-format-output-dir/small-bed/targeted-coverage-nf-1.0.0-rc.1/BZPRGPT1000001-N001-B01-F/
• Case 3: small BAM + large BED
  • sample: A-mini S2.T-n1
  • input yaml: /hot/user/nzeltser/pipeline-targeted-coverage/test/input/a-mini-n1.yaml
  • config: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-format-output-dir/large-bed/targeted-coverage-nf-1.0.0-rc.1/A-mini-n1/
• Case 4: large BAM + large BED
  • sample: BZPRGPT1000001-N001-B01-F
  • input yaml: /hot/user/nzeltser/pipeline-targeted-coverage/test/input/BZPRGPT1000001-N001-B01-F.yaml
  • config: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-format-output-dir/large-bed/targeted-coverage-nf-1.0.0-rc.1/BZPRGPT1000001-N001-B01-F/

Checklist

• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.

• [X] 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].

• [X] I have set up or verified the branch protection rule following the github standards before opening this pull request.

• [X] I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, 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.md under the next release version or unreleased, and updated the date.

• [X] I have updated the version number in the metadata.yaml and manifest block of the nextflow.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.)

• [X] I have tested the pipeline on at least one A-mini sample.