Commit 57820b3e authored by Celine Noirot's avatar Celine Noirot
Browse files

Join channel to avoid mismatch of input files

parent 52f47579
......@@ -750,13 +750,14 @@ process reads_alignment_on_contigs {
depth_on_contigs_ch = contigs_bed_ch.join(reads_assembly_ch_for_depth)
process depth_on_contigs {
tag "${replicateId}"
publishDir "${params.outdir}/05_alignment/05_1_reads_alignment_on_contigs/$replicateId", mode: 'copy'
set val(replicateId), file(bam), file(index) from reads_assembly_ch_for_depth
set replicateId, file(bed) from contigs_bed_ch
set val(replicateId), file(bed) , file(bam), file(index) from depth_on_contigs_ch
set val(replicateId), file("${replicateId}.regions.bed.gz") into contig_depth_ch
......@@ -1071,7 +1072,7 @@ process make_functional_annotation_tables {
* Create channel with sample id, diamond files and desman length files, idxstats and depth files.
diamond_parser_input_ch = diamond_result_ch.join(contigs_length_ch, remainder: true).join(idxstats_ch, remainder: true)
diamond_parser_input_ch = diamond_result_ch.join(contigs_length_ch, remainder: true).join(idxstats_ch, remainder: true).join(contig_depth_ch, remainder: true)
// Python parser.
process diamond_parser {
......@@ -1083,8 +1084,7 @@ process diamond_parser {
set file(prot_accession2taxid), file(taxonomy) from taxonomy_ch
set replicateId, file(diamond_file), file(contigs_len), file(idxstats) from diamond_parser_input_ch
set replicateId, file(depth) from contig_depth_ch
set replicateId, file(diamond_file), file(contigs_len), file(idxstats), file(depth) from diamond_parser_input_ch
set replicateId, file("${replicateId}.percontig.tsv") into taxo_percontig_ch
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