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add msgfdb_indexing #374

Merged
merged 4 commits into from
May 16, 2024
Merged

add msgfdb_indexing #374

merged 4 commits into from
May 16, 2024

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daichengxin
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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/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 15, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 55c8d3b

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-15 06:06:15

@daichengxin daichengxin linked an issue May 15, 2024 that may be closed by this pull request
We should create a database for all the msgf+ jobs #367
Closed
@ypriverol ypriverol requested review from jpfeuffer and ypriverol and removed request for jpfeuffer May 15, 2024 10:34
@ypriverol ypriverol merged commit d64652b into bigbio:dev May 16, 2024
18 checks passed
jpfeuffer
jpfeuffer reviewed May 16, 2024
View reviewed changes
modules/local/openms/thirdparty/msgfdb_indexing/main.nf
@@ -0,0 +1,36 @@
process MSGFDBINDEXING {
tag "$database.baseName"
label 'process_low'
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Not sure if process_low is a good fit. But we will see while we use it.

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Cool looks good

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@jpfeuffer jpfeuffer jpfeuffer left review comments

@ypriverol ypriverol ypriverol approved these changes

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We should create a database for all the msgf+ jobs
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@daichengxin @jpfeuffer @ypriverol