Skip to content

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

Merged
ypriverol merged 19 commits intobigbio:diannfrom
daichengxin:diann
May 17, 2022
Merged

Restruct DIA-NN step 3,4,5#179
ypriverol merged 19 commits intobigbio:diannfrom
daichengxin:diann

Conversation

@daichengxin
Copy link
Collaborator

@daichengxin daichengxin commented May 9, 2022 •
edited by jpfeuffer
Loading

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).

@github-actions
Copy link

github-actions bot commented May 9, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7aaa308

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

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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

@ypriverol
Copy link
Member

ypriverol commented May 9, 2022

This comment is stopping the PR #164 (comment)

jpfeuffer
jpfeuffer reviewed May 9, 2022
View reviewed changes
modules/local/librarygeneration/meta.yml
@@ -1,48 +0,0 @@
name: librarygeneration
Copy link
Collaborator

@jpfeuffer jpfeuffer May 9, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why delete this file?

jpfeuffer
jpfeuffer reviewed May 9, 2022
View reviewed changes
modules/local/diann_preliminary_analysis/main.nf
${time_corr_only} \\
$args \\
|& tee diann.log
|& tee ${mzML.baseName}_diann.log
Copy link
Collaborator

@jpfeuffer jpfeuffer May 9, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
@jpfeuffer
Copy link
Collaborator

jpfeuffer commented May 14, 2022

LFQ failing. See my other msstats issue.

jpfeuffer
jpfeuffer reviewed May 16, 2022
View reviewed changes
Copy link
Collaborator

@jpfeuffer jpfeuffer left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the msstats fix. Please link the issue.

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
Closed
@jpfeuffer
Copy link
Collaborator

jpfeuffer commented May 16, 2022

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.

@daichengxin
Copy link
Collaborator Author

daichengxin commented May 16, 2022 •
edited
Loading

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
.

@jpfeuffer
Copy link
Collaborator

jpfeuffer commented May 16, 2022

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.

@jpfeuffer
Copy link
Collaborator

jpfeuffer commented May 16, 2022

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
Closed
@jpfeuffer
Copy link
Collaborator

jpfeuffer commented May 17, 2022

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jpfeuffer jpfeuffer jpfeuffer left review comments

Assignees

No one assigned

Labels

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

DIANN changes in the current pipeline

3 participants

@daichengxin @ypriverol @jpfeuffer