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Display message when error 132 found #6675

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merged 8 commits into from
Sep 20, 2024
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Merged

Display message when error 132 found #6675

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fd0aed8
Display message when error 132 found
JoseEspinosa Sep 20, 2024
a0d8e55
Update snapshots
JoseEspinosa Sep 20, 2024
be7a7e8
Make lint happy
JoseEspinosa Sep 20, 2024
c38febf
Add call to the function with trap
JoseEspinosa Sep 20, 2024
0a4197e
Make nf-core lint happy
JoseEspinosa Sep 20, 2024
e43c49a
Merge branch 'master' into patch_kalign
JoseEspinosa Sep 20, 2024
95ba3ba
More linting
JoseEspinosa Sep 20, 2024
bd7d9f5
Make lint happy
JoseEspinosa Sep 20, 2024
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12 changes: 12 additions & 0 deletions modules/nf-core/kalign/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,18 @@ process KALIGN_ALIGN {
def prefix = task.ext.prefix ?: "${meta.id}"
def write_output = compress ? ">(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "${prefix}.aln"
"""
error_handler() {
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exit_code=\$?
if [ \$exit_code -eq 132 ]; then
echo "\n\nKALIGN failed because is incompatible with some CPU types, see https://github.com/TimoLassmann/kalign/issues/46.\n\n"
else
trap - ERR
return \$exit_code
fi
}

trap 'error_handler' ERR

unpigz -cdf $fasta | \\
kalign \\
$args \\
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20 changes: 14 additions & 6 deletions modules/nf-core/kalign/align/tests/main.nf.test.snap
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Expand Up @@ -11,7 +11,7 @@
]
],
"1": [
"versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
"versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
],
"alignment": [
[
Expand All @@ -22,11 +22,15 @@
]
],
"versions": [
"versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
"versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
]
}
],
"timestamp": "2024-03-22T16:42:01.934768"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-09-20T12:44:18.067352"
},
"SARS-CoV-2 scaffolds fasta - compressed": {
"content": [
Expand All @@ -40,7 +44,7 @@
]
],
"1": [
"versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
"versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
],
"alignment": [
[
Expand All @@ -51,10 +55,14 @@
]
],
"versions": [
"versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
"versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
]
}
],
"timestamp": "2024-03-22T16:42:07.734293"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-09-20T12:44:31.031883"
}
}
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