From 7b0bfd82d5184e016c47bf31a63b61a188e885ef Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Mon, 10 Feb 2020 21:53:46 -0500 Subject: [PATCH] make sure one file is used in collapse step this is related to UMI in the fastq files. Address: https://github.com/nf-core/smrnaseq/issues/35 --- main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f400b181..ca2085e2 100644 --- a/main.nf +++ b/main.nf @@ -396,13 +396,14 @@ process collapse { file reads from trimmed_reads_collapse output: - file 'collapsed/*.fastq' into collapsed_fasta + file 'final/*.fastq' into collapsed_fasta script: prefix = reads.toString() - '_trimmed.fq.gz' """ seqcluster collapse -f $reads -m 1 --min_size 15 -o collapsed - mv collapsed/${prefix}_trimmed_trimmed.fastq collapsed/${prefix}.fastq + mkdir final + mv collapsed/${prefix}_trimmed_trimmed.fastq final/${prefix}.fastq """ }