diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf index e7d0e4225e5529d177148a8e4b558e51e3d70ffe..53396918b74097b98df5d693a5d04db8ec5b719c 100644 --- a/src/arriba_fusion.nf +++ b/src/arriba_fusion.nf @@ -184,9 +184,9 @@ workflow { mapping2fusion(index_file.collect(), fastp.out.fastq) } filter_bam_quality(mapping2fusion.out.bam) - index_bam(filter_bam_quality.out.bam) + index_bam(filter_bam_quality.out.bam.collect()) arriba(filter_bam_quality.out.bam, gtf_file.collect(), genome_file.collect()) - draw_fusions(arriba.out.fusions, filter_bam_quality.out.bam, gtf_file, index_bam.out.bai) + draw_fusions(arriba.out.fusions, filter_bam_quality.out.bam, gtf_file, index_bam.out.bam_idx) } else { index_bam(bam_files.collect())