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update config to enable usage of a custom config #1108

Merged
merged 7 commits into from
Nov 10, 2023
Merged

update config to enable usage of a custom config #1108

merged 7 commits into from
Nov 10, 2023

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maxulysse
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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/rnaseq 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 Nov 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c8b399

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-09 17:31:25

mahesh-panchal
mahesh-panchal reviewed Nov 9, 2023
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conf/modules.config Outdated
@@ -41,8 +41,8 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.save_reference
pattern: "{!versions.yml}",
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This doesn't work for me. See your tools PR

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yeah, I saw...

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I am sadness

@pinin4fjords pinin4fjords added this to the 3.12.1 milestone Nov 9, 2023
pinin4fjords
pinin4fjords approved these changes Nov 9, 2023
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LGTM in theory. Haven't tested it, but tests passing and I'm due to run a test of the file complement before release anyway.

@maxulysse maxulysse merged commit f189c95 into nf-core:dev Nov 10, 2023
26 checks passed
@maxulysse maxulysse deleted the config_update branch November 10, 2023 08:08
mahesh-panchal
mahesh-panchal reviewed Nov 10, 2023
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Seems a couple of bits were accidentally removed.

conf/modules.config
@@ -167,19 +155,13 @@ process {
ext.args = '--record-count 1000000 --seed 1'
ext.prefix = { "${meta.id}.subsampled" }
publishDir = [
path: { "${params.outdir}/sample_fastq/fastq" },
mode: params.publish_dir_mode,
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Mode looks accidentally deleted here.

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@maxulysse will fix in other PRs- thanks @mahesh-panchal !

conf/modules.config
enabled: false
]
}

withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
ext.args = '--skipQuant'
publishDir = [
path: { "${params.outdir}/sample_fastq/salmon" },
mode: params.publish_dir_mode,
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And here.

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@mahesh-panchal mahesh-panchal mahesh-panchal left review comments

@pinin4fjords pinin4fjords pinin4fjords approved these changes

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3 participants
@maxulysse @pinin4fjords @mahesh-panchal