The same thing as mentioned here by Maxime now als...
# lintingc
Christopher Mohr
03/20/2024, 8:04 AMThe same thing as mentioned here by Maxime now also happened in smrnaseq: https://github.com/nf-core/smrnaseq/actions/runs/8347388799/job/22846889384. Does anyone know why?
https://nfcore.slack.com/archives/CE6PELWR4/p1709913396145279?thread_ts=1709203140.708549&cid=CE6PELWR4
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Maxime Garcia
03/20/2024, 8:17 AMso you didn't update any thing, and suddenly nf-core lint started complaining about this subworkflow?
Maxime Garcia
03/20/2024, 8:20 AMI'd say two people complaining about a similar bug, that's enough to create an issue on github
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Christopher Mohr
03/20/2024, 8:20 AMExactly, I just changed one line in a local module and ran lint afterwards
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Maxime Garcia
03/20/2024, 8:23 AM😱
Maxime Garcia
03/20/2024, 8:23 AM@mashehu @Júlia Mir linting appears to be broken with #C03D38JNFNJ
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mashehu
03/20/2024, 8:54 AMcan you run
nf-core verbose lintc
Christopher Mohr
03/20/2024, 8:58 AMsure, should I just send the whole log as a file?
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mashehu
03/20/2024, 9:00 AMyes, please
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Christopher Mohr
03/20/2024, 9:02 AMverbose_lint_subworkflow_failed.txt
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mashehu
03/20/2024, 9:04 AMi don’t see the error here, which command did you use to get the error?
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Christopher Mohr
03/20/2024, 9:09 AMnow everything should be in there, sorry
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mashehu
03/20/2024, 9:13 AMcan you update
bam_sort_stats_samtoolsc
Christopher Mohr
03/20/2024, 9:18 AMI already did here (https://github.com/nf-core/smrnaseq/pull/328), basically reinstalled it, afterwards I also had to update samtools/SORT
Christopher Mohr
03/20/2024, 9:21 AMor do mean if
updatem
mashehu
03/20/2024, 9:22 AMyes
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Christopher Mohr
03/20/2024, 9:23 AMI'll check
Christopher Mohr
03/20/2024, 9:26 AMSeems to work
Copy code
gitpod /workspace/nf-core-smrnaseq (test_update_subwf) $ nf-core subworkflows update
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13.1 - <https://nf-co.re>
? Update all subworkflows or a single named subworkflow? Named subworkflow
? Subworkflow name: bam_sort_stats_samtools
? Do you want to view diffs of the proposed changes? No previews, just update everything
INFO Updating 'nf-core/bam_sort_stats_samtools'
WARNING All modules and subworkflows linked to the updated subworkflow will be automatically updated.
It is advised to keep all your modules and subworkflows up to date.
It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.
? Would you like to continue updating all modules and subworkflows? No
INFO Updates complete ✨
gitpod /workspace/nf-core-smrnaseq (test_update_subwf) $ git status
On branch test_update_subwf
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git restore <file>..." to discard changes in working directory)
modified: modules.json
modified: subworkflows/nf-core/bam_sort_stats_samtools/main.nfChristopher Mohr
03/20/2024, 9:27 AMlintm
mashehu
03/20/2024, 9:28 AMwin?
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Christopher Mohr
03/20/2024, 9:47 AMdoes it make sense that it fails because of the remote changes? 🤔
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mashehu
03/20/2024, 9:50 AMit is a bug in tools that we somehow don’t catch the correct error, but it is a pain to reproduce, tbh. but you can open an issue on tools with it and also clear description how you had set it up before we fixed it 🙂
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Christopher Mohr
03/20/2024, 10:00 AMOnly if you think it makes sense / would be helpful. I mean it seems to be easy to fix if it happens, I was just wondering if it might be a "systematic" issue that might need some more attention.
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mashehu
03/20/2024, 10:00 AMyes, since you are the second person running into it, I would call it systemic 🙂
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