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Correct non-gzipped output from clustalo/align #7197

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Dec 11, 2024
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Correct non-gzipped output from clustalo/align #7197

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2 changes: 1 addition & 1 deletion modules/nf-core/clustalo/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ process CLUSTALO_ALIGN {
def fhmm_batch = hmm_batch ? "--hmm-batch=${hmm_batch}" : ""
def fprofile1 = profile1 ? "--profile1=${profile1}" : ""
def fprofile2 = profile2 ? "--profile2=${profile2}" : ""
def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln"
def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "-o ${prefix}.aln"
// using >() is necessary to preserve the return value,
// so nextflow knows to display an error when it failed
// the --force -o is necessary, as clustalo expands the commandline input,
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