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Chromap patch (#712)
* Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remove samtools version * Add space * Remove whitespace
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1 changed files with 2 additions and 2 deletions
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@ -64,8 +64,6 @@ process CHROMAP_CHROMAP {
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samtools view $options.args2 -@ ${task.cpus} -bh \\
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-o ${prefix}.bam ${prefix}.${file_extension}
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rm ${prefix}.${file_extension}
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samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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if (meta.single_end) {
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@ -76,6 +74,7 @@ process CHROMAP_CHROMAP {
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-r $fasta \\
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-1 ${reads.join(',')} \\
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-o ${prefix}.${file_extension}
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echo "$VERSION" > ${software}.version.txt
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""" + compression_cmds
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} else {
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@ -87,6 +86,7 @@ process CHROMAP_CHROMAP {
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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-o ${prefix}.${file_extension}
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echo "$VERSION" > ${software}.version.txt
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""" + compression_cmds
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}
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