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fixed multiple bugs and nf-template #331

Merged
merged 15 commits into from
Dec 27, 2023
Merged

fixed multiple bugs and nf-template #331

merged 15 commits into from
Dec 27, 2023

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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 (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).

@daichengxin daichengxin linked an issue Dec 21, 2023 that may be closed by this pull request
Warning message should be removed #322
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github-actions bot commented Dec 21, 2023 •
edited
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nf-core lint overall result: Passed ✅

Posted for pipeline commit e80ba58

+| ✅ 160 tests passed       |+
#| ❔   4 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2023-12-27 07:57:48

@ypriverol
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@jpfeuffer can we move the phospho files to PRIDE FTP.

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I would say put it to wherever is most reliable.

Did you see this: nf-core#134

Also seems to be related to test data

@daichengxin daichengxin linked an issue Dec 24, 2023 that may be closed by this pull request
SAGE jobs are not caching #326
Closed
@daichengxin daichengxin linked an issue Dec 26, 2023 that may be closed by this pull request
DIA-NN convert to mzTab failing #333
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ypriverol
ypriverol requested changes Dec 26, 2023
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bin/diann_convert.py Outdated
@@ -825,7 +825,7 @@ def mztab_PSH(report, folder, database):
def __find_info(directory, n):
# This line matches n="220101_myfile", folder="." to
# "myfolder/220101_myfile_ms_info.tsv"
files = list(Path(directory).glob(f"*{n}*_info.tsv"))
files = list(Path(directory).glob(f"{n}_ms_info.tsv"))
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@ypriverol ypriverol Dec 26, 2023 •
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@daichengxin I think is better:

files = list(Path(directory).rglob(f"{n}_ms_info.tsv"))

This will allow to search in subfolders.

@daichengxin daichengxin changed the title fixed multiqc warning and nf-template fixed multiple bugs and nf-template Dec 27, 2023
@daichengxin daichengxin mentioned this pull request Dec 27, 2023
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@ypriverol ypriverol self-requested a review December 27, 2023 18:53
@ypriverol ypriverol merged commit d770c74 into bigbio:dev Dec 27, 2023
12 of 17 checks passed
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@ypriverol ypriverol ypriverol approved these changes

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Successfully merging this pull request may close these issues.

DIA-NN convert to mzTab failing SAGE jobs are not caching Warning message should be removed
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@daichengxin @ypriverol @jpfeuffer @nf-core-bot