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Chromograph viz #507

Merged
merged 5 commits into from
Feb 2, 2024
Merged

Chromograph viz #507

merged 5 commits into from
Feb 2, 2024

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ramprasadn
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PR checklist

Addresses #495

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b1f0c84

+| ✅ 178 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • 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
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 13:18:56

@ramprasadn ramprasadn marked this pull request as ready for review February 1, 2024 16:22
@ramprasadn ramprasadn requested a review from jemten February 2, 2024 10:10
jemten
jemten reviewed Feb 2, 2024
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Looks good, one small comment on the outfiles

conf/modules/qc_bam.config
@@ -50,6 +50,11 @@ process {
ext.args = '-clip'
}

withName: '.*QC_BAM:CHROMOGRAPH_COV' {
ext.args = '--euploid --step 500'
ext.prefix = { "${meta2.id}_chromographcov" }
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We want to publish this directory as it contains the plots. We should also describe the outfiles

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All outputs from the qc bam subworkflow are published by default. I will update the documentation now.

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I have updated the document now.

@ramprasadn ramprasadn requested a review from jemten February 2, 2024 13:17
jemten
jemten approved these changes Feb 2, 2024
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👍

@ramprasadn ramprasadn merged commit 4942bde into nf-core:dev Feb 2, 2024
6 checks passed
@ramprasadn ramprasadn deleted the chromograph_viz branch February 2, 2024 16:56
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten