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Refactor CAT_FASTQ to ignore number of files input

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Thomas A. Christensen II 2022-05-16 17:44:47 -05:00
parent 4eca77d63b
commit 57129daf52
1 changed files with 25 additions and 22 deletions
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47
modules/cat/fastq/main.nf
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@ -21,31 +21,34 @@ process CAT_FASTQ {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def readList = reads.collect{ it.toString() } def readList = reads.collect{ it.toString() }
// Groovy gotcha: files are iterable, so we can't check for a single file
// using reads.length or something similar. The way we *can* tell if we are
// iterating through a file is to check if the first object is a file.
// If iterating a file, the first object will not be a file, and will
// instead represent the directory. In that case, use a path separator when
// joining the list in the commands.
def joiner = !reads.first().isFile() ? '/' : ' '
if (meta.single_end) { if (meta.single_end) {
if (readList.size > 1) { """
""" cat ${readList.join(joiner)} > ${prefix}.merged.fastq.gz
cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
}
} else { } else {
if (readList.size > 2) { def read1 = []
def read1 = [] def read2 = []
def read2 = [] readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } """
""" cat ${read1.join(joiner)} > ${prefix}_1.merged.fastq.gz
cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz cat ${read2.join(joiner)} > ${prefix}_2.merged.fastq.gz
cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
}
} }
} }