diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf index 63cb663343246cad39e8d6e4b1aa2baffdcf1d34..0567db4b57c619e37cf87892b129a2c1e6718601 100644 --- a/src/RNAseq_XGR.nf +++ b/src/RNAseq_XGR.nf @@ -160,11 +160,11 @@ workflow { // ref_13 = Channel.fromPath(params.idx +'/transcriptInfo.tab') // ref_14 = Channel.fromPath(params.idx +'/sjdbList.fromGTF.out.tab') // ref_15 = Channel.fromPath(params.idx +'/sjdbList.out.tab') - // genome_indexed_input = ref_1.concat(ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8,ref_9,ref_10,ref_11,ref_12,ref_13,ref_14,ref_15) - // Channel - // .of( idx_genome ) - // .set { genome_indexed_input } + + Channel + .fromPath( "${params.idx}/*" ) + .set { genome_indexed_input } mapping_withindex(idx_genome, fastp.out.fastq) stats_bam(mapping_withindex.out.bam) filter_bam_mapped(mapping_withindex.out.bam) diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf index 91a74dc4ec912e8ee633d00035beaccbc9838840..ac4a4fdb047c7e3d5f5c4974d72881ade315d77a 100644 --- a/src/nf_modules/star/main_2.7.8a.nf +++ b/src/nf_modules/star/main_2.7.8a.nf @@ -193,7 +193,7 @@ process mapping_withindex { } input: - val(index) + path(index) tuple val(reads_id), path(reads) output: