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Add options for saving intermediate files #314

Merged
merged 5 commits into from
Feb 9, 2024
Merged

Add options for saving intermediate files #314

merged 5 commits into from
Feb 9, 2024

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christopher-mohr
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This

  • adds a new parameter save_aligned to specify whether to store aligned reads (of GENOME_QUANT:BOWTIE_MAP_GENOME)
  • activates the already exisiting paramter save_merged
  • sets save_aligned to false for test profile

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Feb 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7d0a749

+| ✅ 182 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-09 08:49:49

@apeltzer apeltzer merged commit 4791cf9 into nf-core:dev Feb 9, 2024
8 checks passed
@christopher-mohr christopher-mohr deleted the save_intermediate_optional branch February 9, 2024 09:26
@apeltzer apeltzer mentioned this pull request Feb 22, 2024
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2 participants
@christopher-mohr @apeltzer