Commit 36711f28 authored by Brandi Cantarel's avatar Brandi Cantarel

update trim for se

parent ff1544dd
Pipeline #7607 failed with stage
in 11 seconds
......@@ -61,13 +61,13 @@ if (params.pairs == 'pe') {
spltnames
.splitCsv()
.filter { fileMap.get(it[1]) != null & fileMap.get(it[2]) != null }
.map { it -> tuple(it[0], fileMap.get(it[1]), fileMap.get(it[2])) }
.map { it -> tuple(it[0], [fileMap.get(it[1]), fileMap.get(it[2])]) }
.set { read }
} else {
spltnames
.splitCsv()
.filter { fileMap.get(it[1]) != null }
.map { it -> tuple(it[0], fileMap.get(it[1]),'') }
.map { it -> tuple(it[0], [fileMap.get(it[1])]) }
.set { read }
}
if( ! read ) { error "Didn't match any input files with entries in the design file" }
......@@ -76,13 +76,13 @@ if( ! read ) { error "Didn't match any input files with entries in the design fi
process trim {
errorStrategy 'ignore'
input:
set pair_id, file(read1), file(read2) from read
set pair_id, file(fqs) from read
output:
set pair_id, file("${pair_id}.trim.R1.fastq.gz"),file("${pair_id}.trim.R2.fastq.gz") into trimread
set pair_id, file("${pair_id}.trim.R1.fastq.gz"),file("${pair_id}.trim.R2.fastq.gz") into fusionfq
script:
"""
bash $baseDir/process_scripts/preproc_fastq/trimgalore.sh -p ${pair_id} -a ${read1} -b ${read2}
bash $baseDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
"""
}
......
Subproject commit 16061b5a505657cb2c8055091df582c4a75137f5
Subproject commit 529fdbfc477dcb0d2c5879e82f6175ea1dae818c
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