add MSstatsTMT and update MSstats #158

daichengxin · 2022-04-22T14:24:52Z

PR checklist

u

github-actions · 2022-04-22T14:25:54Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 91f0ac9

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

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0'

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config

✅ Tests passed:

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schema_lint - Schema lint passed
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merge_markers - No merge markers found in pipeline files
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Run details

nf-core/tools version 2.3.2
Run at 2022-04-26 08:52:28

nextflow.config

ypriverol · 2022-04-23T06:33:13Z

@daichengxin MSstats is failing with DIANN

daichengxin · 2022-04-23T06:34:43Z

ok. I am testing locally.

ypriverol · 2022-04-23T06:36:46Z

I think is because in the last tests we have included only two files in the DIANN with no multiple conditions. But this is only a guess.

daichengxin · 2022-04-23T07:00:27Z

Yes. you are right. I use two conditions locally to test. Need to update the test data

daichengxin · 2022-04-23T11:22:49Z

The test passed. Need to upload the latest dia test data to nfcore, then recover test_dia config. https://raw.githubusercontent.com/daichengxin/quantms/dev/assets/PXD026600.sdrf.tsv

jpfeuffer · 2022-04-26T07:01:53Z

Why are you not using the newest version with argument parsing? Because of the additional dependency?
https://github.com/nf-core/proteomicslfq/blob/dev/bin/msstats_plfq.R

daichengxin · 2022-04-26T07:06:02Z

Yes. argparse is not in the container

bin/msstats_plfq.R

Co-authored-by: Julianus Pfeuffer <[email protected]>

bin/msstats_tmt.R

Co-authored-by: Julianus Pfeuffer <[email protected]>

jpfeuffer · 2022-04-26T08:52:34Z

Can we maybe have the logging changes separate? I don't think this is ready for release.

jpfeuffer · 2022-04-26T08:56:42Z

E.g. it needs a lot of testing, the testdata needs to be on nf-core, I think it is better to only have one MSstats step/script (we need to check whether there are more parameters that we can combine).

daichengxin · 2022-04-26T12:15:51Z

So do we need to remove the logging changes in this PR?

jpfeuffer · 2022-04-26T12:16:35Z

No but create a PR with just the logging changes.

jpfeuffer · 2022-04-26T12:16:52Z

Use git cherry-pick on a new branch

ypriverol · 2022-04-27T13:16:50Z

Can I merge this PR @jpfeuffer ?

jpfeuffer · 2022-04-27T13:17:34Z

No, see my comments

ypriverol · 2022-04-27T13:20:31Z

We need two different PRs? Why we can combine both changes here if they are correct.

jpfeuffer · 2022-04-27T13:21:39Z

because then we have to wait until everything else is correct. MSstats is not a priority. A working pipeline is.

ypriverol · 2022-04-27T13:26:41Z

But @daichengxin changed the MSstats as requested, then both things are OK now.

jpfeuffer · 2022-04-27T13:27:32Z

E.g. it needs a lot of testing, the testdata needs to be on nf-core, I think it is better to only have one MSstats step/script (we need to check whether there are more parameters that we can combine).

We need more param combinations to be tested. Plus the rest of the comment.

ypriverol · 2022-04-27T13:32:26Z

We need two things here:

load the testdata into nf-core, this is mainly the SDRF of the DIANN tests.
increase the test coverage for MSstats.

Can we, merge this PR and do another one replacing the SDRF and loading into NF-core and add an issue in the future for more testing? I just want to be able to contribute now.

jpfeuffer · 2022-04-27T13:33:57Z

You can contribute to this PR. I just want to merge into master soon, and do not want to have half-ready PRs in there.

daichengxin · 2022-04-29T09:04:28Z

I got the changes that needs to be done. But I'm afraid I won't be able to do it soon because I'm not very familiar with the mechanics of CI.

jpfeuffer and others added 10 commits April 21, 2022 14:25

require outdir

0ad8a73

require more params

4f19874

Update branch.yml

39e5a26

Update branch.yml

f084ab6

Revert...

48ad4b6

Update branch.yml

99be205

Update branch.yml

b42e28a

Update branch.yml

1193c6e

Merge pull request #4 from nf-core/dev

f8ed074

u

Add MSstatsTMT and update MSstats

a773f96

lint

5c6c851

jpfeuffer requested changes Apr 22, 2022

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daichengxin added 3 commits April 23, 2022 17:22

update

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update log info

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daichengxin linked an issue Apr 26, 2022 that may be closed by this pull request

Reevaluate logging #160

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jpfeuffer reviewed Apr 26, 2022

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Update bin/msstats_plfq.R

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Co-authored-by: Julianus Pfeuffer <[email protected]>

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Update bin/msstats_tmt.R

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Co-authored-by: Julianus Pfeuffer <[email protected]>

ypriverol mentioned this pull request Apr 28, 2022

add conda test #162

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jpfeuffer merged commit ae9c934 into bigbio:dev Apr 29, 2022

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add MSstatsTMT and update MSstats #158

add MSstatsTMT and update MSstats #158

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add MSstatsTMT and update MSstats #158

add MSstatsTMT and update MSstats #158

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daichengxin commented Apr 22, 2022

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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`nf-core lint` overall result: Passed ✅ ⚠️

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