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Multiple entry points: add BAM inputs #383

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wants to merge 7 commits into from
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Multiple entry points: add BAM inputs #383

wants to merge 7 commits into from

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fa2k
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@fa2k fa2k commented Jul 20, 2023

Issue #261.

A new parameter --input-type is added, which can be reads for the existing fastq input, or alignments to use a duplicate-marked bam file as input.

This change splits the CHECK_INPUT subworkflow into separate workflows for bam and FASTQ.

check_sample_sheet.py is generalised to work with an alternative sample sheet format without fastq_[12], columns, with bam instead.

Conditionals are added in the main workflow raredisease.nf to enable processing of bam files.

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!

New pipeline profile test_bam is added.

4 warnings & 9 fail; do not seem related to the changes in this PR.

  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).

Tests fail, but it doesn't seem related to the change. I will submit an issue about this.

  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

Will update when I find the PR number.

  • README.md is updated (including new tool citations and authors/contributors). | No new tools.

fa2k added 5 commits May 30, 2023 12:03
@fa2k
Initial version of the bam input_type
ff78904
@fa2k
Merge remote-tracking branch 'upstream/master' into multiple-entry-po…
c3fd9e5 
…ints
@fa2k
Fix so it works for bam and fastq inputs (Sample sheet Check/IDs)
7fa21da
@fa2k
Merge remote-tracking branch 'upstream/dev' into multiple-entry-points
36791bf 
Merged conflicting changes in
* raredisease.nf
* nextflow_schema.json
* check_sample_sheet.py

Conflicts were related to changed arguments, general restructuring of the workflow,
and checking for case_id in sample sheet.
@fa2k
Refer to bam file PR
4065cfe
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github-actions bot commented Jul 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 27f1af2

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-24 12:11:22

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fa2k commented Nov 15, 2023

Try again later :)

@fa2k fa2k closed this Nov 15, 2023
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