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Restruct DIA-NN step 3,4,5 #179

Merged
merged 19 commits into from
May 17, 2022
Merged

Restruct DIA-NN step 3,4,5 #179

merged 19 commits into from
May 17, 2022

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daichengxin
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@daichengxin daichengxin commented May 9, 2022 •
edited by jpfeuffer
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fixes #164

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 9, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7aaa308

+| ✅ 145 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-05-17 13:34:19

@ypriverol
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This comment is stopping the PR #164 (comment)

jpfeuffer
jpfeuffer reviewed May 9, 2022
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modules/local/librarygeneration/meta.yml
@@ -1,48 +0,0 @@
name: librarygeneration
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Why delete this file?

jpfeuffer
jpfeuffer reviewed May 9, 2022
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modules/local/diann_preliminary_analysis/main.nf
@@ -52,7 +52,7 @@ process DIANN_PRELIMINARY_ANALYSIS {
${quick_mass_acc} \\
${time_corr_only} \\
$args \\
|& tee diann.log
|& tee ${mzML.baseName}_diann.log
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I feel like --gen-spec-lib should not be here but let's wait for input

@daichengxin daichengxin changed the title Assemble empirical library Restruct DIA-NN step 3,4,5 May 14, 2022
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LFQ failing. See my other msstats issue.

jpfeuffer
jpfeuffer reviewed May 16, 2022
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Thanks for the msstats fix. Please link the issue.

bin/msstats_plfq.R Outdated Show resolved Hide resolved
bin/msstats_tmt.R Outdated Show resolved Hide resolved
daichengxin and others added 2 commits May 16, 2022 15:07
@daichengxin @jpfeuffer
Update bin/msstats_plfq.R
831f2b9 
Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>
@daichengxin @jpfeuffer
Update bin/msstats_tmt.R
0abac0b 
Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>
@daichengxin daichengxin mentioned this pull request May 16, 2022
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Looks VERY good from my side. The only thing I noticed, is that the results from the workflow that are uploaded in the GitHub Action (https://github.com/bigbio/quantms/actions/runs/2330274194) are 4GB for DIA 😆 We should reduce this. Do you think those are all important intermediate results? If so, we should change the config of the test profile. If not, just do not publish them with publishDir.

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daichengxin commented May 16, 2022 •
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The converted mzML files has accounted for 4G. They may need to be preserved
2022-05-16 18-55-37 的屏幕截图
.

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Hmm yes, we definitely don't need it in CI. We actually could skip conversion by uploading mzML files for CI (which might also make it a bit faster). I think conversion is tested in the phospho CI step already.
Let me discuss with @ypriverol about the defaults.

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Can you also add IDs to some of the steps that are missing it?

[1f/58c543] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:SILICOLIBRARYGENERATION (1)
[11/e83042] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS (RD139_Narrow_UPS1_0_1fmol_inj2)
[26/815e8d] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS (RD139_Narrow_UPS1_0_1fmol_inj1)
[63/fb6221] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS (RD139_Narrow_UPS1_0_25fmol_inj1)
[26/b936c2] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS (RD139_Narrow_UPS1_0_25fmol_inj2)
[74/35cf3d] Submitted process > NFCORE_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS (1)
[05/e66ccb] Submitted process > NFCORE_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY (1)
```

@jpfeuffer jpfeuffer linked an issue May 16, 2022 that may be closed by this pull request
DIANN changes in the current pipeline #164
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Hi @daichengxin we decided that we will keep the converted mzmls by default. Can you add a config that "deletes" the publishDir in the Thermorawfileparser step for the test_dia profile?

@ypriverol ypriverol merged commit 86c9026 into bigbio:diann May 17, 2022
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DIANN changes in the current pipeline
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@daichengxin @ypriverol @jpfeuffer