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Chromap patch (#712)

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* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove samtools version

* Add space

* Remove whitespace
This commit is contained in:
Mahesh Binzer-Panchal 2021-09-16 10:23:07 +02:00 committed by GitHub
parent e9c57083a0
commit e904107c22
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1 changed files with 2 additions and 2 deletions
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4
modules/chromap/chromap/main.nf
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@ -64,8 +64,6 @@ process CHROMAP_CHROMAP {
samtools view $options.args2 -@ ${task.cpus} -bh \\ samtools view $options.args2 -@ ${task.cpus} -bh \\
-o ${prefix}.bam ${prefix}.${file_extension} -o ${prefix}.bam ${prefix}.${file_extension}
rm ${prefix}.${file_extension} rm ${prefix}.${file_extension}
samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
""" """
} }
if (meta.single_end) { if (meta.single_end) {
@ -76,6 +74,7 @@ process CHROMAP_CHROMAP {
-r $fasta \\ -r $fasta \\
-1 ${reads.join(',')} \\ -1 ${reads.join(',')} \\
-o ${prefix}.${file_extension} -o ${prefix}.${file_extension}
echo "$VERSION" > ${software}.version.txt echo "$VERSION" > ${software}.version.txt
""" + compression_cmds """ + compression_cmds
} else { } else {
@ -87,6 +86,7 @@ process CHROMAP_CHROMAP {
-1 ${reads[0]} \\ -1 ${reads[0]} \\
-2 ${reads[1]} \\ -2 ${reads[1]} \\
-o ${prefix}.${file_extension} -o ${prefix}.${file_extension}
echo "$VERSION" > ${software}.version.txt echo "$VERSION" > ${software}.version.txt
""" + compression_cmds """ + compression_cmds
} }