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Missing import statements on error messages when starting without samplesheet #1566

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asp8200 opened this issue Jun 13, 2024 · 2 comments
Closed

Missing import statements on error messages when starting without samplesheet #1566

asp8200 opened this issue Jun 13, 2024 · 2 comments
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@pharmlovex
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bug Something isn't working
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3.5

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@asp8200
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asp8200 commented Jun 13, 2024

Description of the bug

When not supplying --input (directly or indirectly through use of profile) in a cmd like

nextflow run nf-core/sarek -r 3.4.2 -profile docker --outdir results

on gets the not-so-informative error msg:

ERROR ~ No such variable: Nextflow

 -- Check script '/home/ubuntu/.nextflow/assets/nf-core/sarek/./subworkflows/local/utils_nfcore_sarek_pipeline/main.nf' at line: 344 or see '.nextflow.log' file for more details

It might not be so straightforward to improve on this, as not all commands for sarek require --input:

https://nfcore.slack.com/archives/C05V9FRJYMV/p1718263762323759?thread_ts=1718262962.010069&cid=C05V9FRJYMV

Command used and terminal output

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@asp8200 asp8200 added the bug Something isn't working label Jun 13, 2024
@FriederikeHanssen FriederikeHanssen added this to the 3.5 milestone Jul 8, 2024
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The issue is, that Nextflow is improperly called in one of the utils subworkflows. Removing it and just call error should fix it.

@FriederikeHanssen FriederikeHanssen changed the title Suboptimal error msg on missing input Missing import statements on error messages when starting without samplesheet Jul 8, 2024
pharmlovex added a commit to pharmlovex/sarek that referenced this issue Oct 29, 2024
@pharmlovex
🐛 Missing import statements on error messages. nf-core#1566
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@pharmlovex pharmlovex self-assigned this Oct 29, 2024
pharmlovex added a commit to pharmlovex/sarek that referenced this issue Oct 29, 2024
@pharmlovex
Fix: Missing import statements on error messages(nf-core#1566)
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@pharmlovex pharmlovex mentioned this issue Oct 29, 2024
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pharmlovex added a commit that referenced this issue Oct 30, 2024
@pharmlovex
Merge pull request #1712 from pharmlovex/dev
8ea4af9 
Fix: Missing import statements on error messages(#1566)
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This issue has been fixed #1712 .

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Hackathon October 2024
Status: Done
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3.5
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@FriederikeHanssen @asp8200 @pharmlovex