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wildcard expansion in vsearch bug fix #8307

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Merged
merged 5 commits into from
Apr 23, 2025
Merged

wildcard expansion in vsearch bug fix #8307

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0cb5cef
wildcard expansion throwing an "arguments too long" error
tom-brekke Apr 15, 2025
387aa5d
Merge pull request #1 from tom-brekke/tom-brekke-patch-1
tom-brekke Apr 15, 2025
15c404c
added -type f to force find to only work on files
tom-brekke Apr 23, 2025
7239818
Merge branch 'master' into master
Joon-Klaps Apr 23, 2025
2be8570
Merge branch 'master' into master
tom-brekke Apr 23, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/vsearch/cluster/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ process VSEARCH_CLUSTER {

if [[ $args3 == "--clusters" ]]
then
gzip -n ${prefix}.${out_ext}*
find . -name \"${prefix}.${out_ext}*[0-9]\" | xargs gzip -n
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I would be consistent throughout, if you've had this issue with --clusters, others might have the same issue with --samout. Also update that one no?

Also is it a given that vsearch always append a single digit to the end of the file?

Might also be could to specify to find that we're looking for files with -type f?

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I added in the -type f good call on that.

The --samout bit doesn't use a wildcard expansion like the --clusters does, so I think it should be ok as is. vsearch outputs many single-entry fastas, one for each centroid, whereas I believe that samtools makes a single multi-entry fasta so no wildcard expansion is needed. Happy to discuss further if I've missed something.

vsearch does append digits to the end when that --clusters flag is set, starting with 0 and counting up where there's one for each cluster centroid:

ASV_post_clustering.clusters.fasta0
ASV_post_clustering.clusters.fasta10000
ASV_post_clustering.clusters.fasta10001
ASV_post_clustering.clusters.fasta10002
ASV_post_clustering.clusters.fasta10003
...

So anchoring the regex with a final trailing digit does match all of those. The gzip then appends .gz and so the files end up looking like

ASV_post_clustering.clusters.fasta0.gz
ASV_post_clustering.clusters.fasta10000.gz
ASV_post_clustering.clusters.fasta10001.gz
ASV_post_clustering.clusters.fasta10002.gz
ASV_post_clustering.clusters.fasta10003.gz
...

which will not be matched again as now they no longer end with a digit.

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Ok great, then it's good to go I believe!

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thank you!

elif [[ $args3 != "--samout" ]]
then
gzip -n ${prefix}.${out_ext}
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