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Update nextflow_schema.json and fix mzTab output #210

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merged 3 commits into from May 6, 2022
Merged

Update nextflow_schema.json and fix mzTab output #210

merged 3 commits into from May 6, 2022

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marissaDubbelaar
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This PR includes a better definition of saving the mzTab files in the Intermediate folder and has an updated nextflow_schema.json to include

PR checklist

  • This comment contains a description of changes (with reason).
  • 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 May 5, 2022 •
edited

nf-core lint overall result: Passed ✅

Posted for pipeline commit b62d6a1

+| ✅ 146 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-06 14:47:05

d4straub
d4straub approved these changes May 6, 2022
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Looks good to me!

conf/modules.config
Comment on lines +137 to +141
withName: 'OPENMS_DECOYDATABASE|OPENMS_THERMORAWFILEPARSER|OPENMS_PEAKPICKERHIRES|OPENMS_PEPTIDEINDEXER|OPENMS_FALSEDISCOVERYRATE|OPENMS_IDMERGER|OPENMS_MAPRTTRANSFORMER.*ML|OPENMS_FEATURE.*|OPENMS_IDCONFLICTRESOLVER' {
publishDir = [ enabled: false ]
}

withName: 'OPENMS_MZTABEXPORTER_QUANT' {
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afaik definitions of OPENMS_MZTABEXPORTER are inherited to OPENMS_MZTABEXPORTER_QUANT because include { OPENMS_MZTABEXPORTER as OPENMS_MZTABEXPORTER_QUANT }. I typically try to avoid specifying the base name (i.e. here OPENMS_MZTABEXPORTER) but rather rename all processes (i.e. use include as) so that those confusions do not happen. Just a comment. In this case here all should go fine.

CHANGELOG.md

### `Fixed`

Resolved the problem that there was no output from `OPENMS_MZTABEXPORTER_QUANT`
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I'd typically add the link to the PR, i.e.

Suggested change
Resolved the problem that there was no output from `OPENMS_MZTABEXPORTER_QUANT`
- [#210](https://github.com/nf-core/mhcquant/pull/210) - Resolved the problem that there was no output from `OPENMS_MZTABEXPORTER_QUANT`

CHANGELOG.md Outdated Show resolved Hide resolved
@marissaDubbelaar @d4straub
Update CHANGELOG.md
b62d6a1 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@marissaDubbelaar marissaDubbelaar merged commit e8da011 into nf-core:dev May 6, 2022
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@marissaDubbelaar @d4straub