From a7d3716ee261c30f9108b7057cbf8dbb57d0e097 Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Thu, 1 Dec 2022 15:36:22 +0100
Subject: [PATCH] arriba_fusion.nf: Add .collect() for index_file, genome_file
& gtf_file
---
src/arriba_fusion.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index 03252a2..c539b2d 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -178,16 +178,16 @@ workflow {
*/
if(params.index == "") {
index_with_gtf(genome_file, gtf_file)
- mapping2fusion(index_with_gtf.out.index, fastp.out.fastq)
+ mapping2fusion(index_with_gtf.out.index.collect(), fastp.out.fastq)
} else {
- mapping2fusion(index_file, fastp.out.fastq)
+ mapping2fusion(index_file.collect(), fastp.out.fastq)
}
filter_bam_quality(mapping2fusion.out.bam)
- arriba(filter_bam_quality.out.bam, gtf_file, genome_file)
+ arriba(filter_bam_quality.out.bam, gtf_file.collect(), genome_file.collect())
// draw_fusions(arriba.out.fusions, filter_bam_quality.out.bam, gtf_file)
}
else {
- arriba(bam_files, gtf_file, genome_file)
+ arriba(bam_files, gtf_file.collect(), genome_file.collect())
// draw_fusions(arriba.out.fusions, bam_files, gtf_file)
}
}
\ No newline at end of file
--
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