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BICF
Astrocyte
rnaseq
Commits
36711f28
Commit
36711f28
authored
Jul 20, 2020
by
Brandi Cantarel
Browse files
update trim for se
parent
ff1544dd
Pipeline
#7607
failed with stage
in 11 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
workflow/main.nf
View file @
36711f28
...
...
@@ -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
}
"""
}
...
...
process_scripts
@
529fdbfc
Compare
16061b5a
...
529fdbfc
Subproject commit
16061b5a505657cb2c8055091df582c4a75137f5
Subproject commit
529fdbfc477dcb0d2c5879e82f6175ea1dae818c
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