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add name of each ID step #176

Merged
merged 17 commits into from
May 6, 2022
Merged

add name of each ID step #176

merged 17 commits into from
May 6, 2022

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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).

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github-actions bot commented May 4, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 8361c38

+| ✅ 144 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-05 17:56:14

@daichengxin daichengxin linked an issue May 4, 2022 that may be closed by this pull request
Have better IDs for every step #171
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@daichengxin daichengxin requested a review from jpfeuffer May 4, 2022 02:55
@jpfeuffer
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jpfeuffer commented May 4, 2022 •
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Very nice. Can we maybe call the output of msstats also after the input SDRF/experimental design?
E.g. pxd000123.mztab
pxd00123_msstats_in.csv

And in the msstats step
pxd000123_msstats_out.csv

If the input was pxd000123.sdrf.tsv

@daichengxin
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You mean when run the msstats step, pxd000123_msstats_out.csv is displayed, right? Because the current msstats doesn't need the sdrf file, it doesn't seem to be able to tag. I probably didn't get what you meant. 😢

@ypriverol
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I guess the name of the output should be based on the sdrf file name. I guess this is the suggestion from @jpfeuffer .

@jpfeuffer
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But if you name the output from ProteomicsLFQ etc based on the experimental design you can also parse that in msstats.

@jpfeuffer
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If the input to msstats is called pxd123_msstats_in.csv then you can just name the output pxd123_msstats_out.csv

@daichengxin
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sorry, Currently msstats does not require an experimental design file or sdrf. So the names of the following outputs need to be dynamically adjusted?

quantms/modules/local/openms/proteomicslfq/main.nf

Lines 15 to 18 in 91ba6c1

output:
path "out.mzTab", emit: out_mztab
path "out.consensusXML", emit: out_consensusXML
path "out_msstats.csv", emit: out_msstats optional true

quantms/modules/local/openms/msstatsconverter/main.nf

Lines 23 to 27 in 91ba6c1

MSstatsConverter \\
-in ${consensusXML} \\
-in_design ${exp_file} \\
-method ${quant_method} \\
-out out_msstats.csv \\

@jpfeuffer
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jpfeuffer commented May 4, 2022 •
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Yes Just use the input names of the exp_design. Yes, dynamically. In PLFQ and MSStatsconverter. Then use those names in Msstats

@jpfeuffer jpfeuffer requested a review from ypriverol May 5, 2022 19:21
@ypriverol ypriverol merged commit 6b54ba3 into bigbio:dev May 6, 2022
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@ypriverol ypriverol ypriverol approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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Have better IDs for every step
3 participants
@daichengxin @jpfeuffer @ypriverol