In some cases RGI will not produce all files expected for mving for publishing

[jfy133]

Description of the bug

https://nfcore.slack.com/archives/C02K5GX2W93/p1715619477736569

Just need to make ,mv. commands only executed if present

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jfy133]

Module in, juyst need to update

[amizeranschi]

Hey @jfy133

Thanks a lot for following up on this issue. I've tested the following replacement for the mv command and it got RGI working fine for me:

for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done

[jfy133]

Oh nice @amizeranschi ! That's much better than my solution...

I updated the module over at nf-core/modules, so you get credit, could you make a PR replacing my horrible copypasta over there and ping me for review? Then we can update the pipeline :)

[amizeranschi]

This should now be fixed by nf-core/modules#5614

[jfy133]

Reopened until update is in pipeline :)