Commit 0a261ff0 authored by Brandi Cantarel's avatar Brandi Cantarel Committed by David Trudgian
Browse files

update single-end part of code

parent bfa008bc
......@@ -31,7 +31,7 @@ Channel
}
.groupTuple(sort: true)
.map { id, files -> tuple(id, files[0],files[1])}
.set { read_pairs }
.set { read_pe }
}
if (params.pairs == 'se') {
Channel
......@@ -43,7 +43,7 @@ Channel
}
.groupTuple(sort: true)
.map { id, files -> tuple(id, files[0])}
.set { read_pairs }
.set { read_se }
}
/*
......@@ -94,7 +94,7 @@ def readPrefix( Path actual, template ) {
//
process trimpe {
input:
set pair_id, file(read1), file(read2) from read_pairs
set pair_id, file(read1), file(read2) from read_pe
output:
set pair_id, file("${read1.baseName.split("\\.", 2)[0]}_val_1.fq.gz"), file("${read2.baseName.split("\\.", 2)[0]}_val_2.fq.gz") into trimpe
when:
......@@ -107,7 +107,7 @@ process trimpe {
}
process trimse {
input:
set pair_id, file(read1) from read_pairs
set pair_id, file(read1) from read_se
output:
set pair_id, file("${read1.baseName.split("\\.", 2)[0]}_trimmed.fq.gz") into trimse
when:
......
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