Join channel to avoid mismatch of input files

main.nf

@@ -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'
 
    input:
-   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 
    output:
    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 {
 
   input:
   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
 
   output:
   set replicateId, file("${replicateId}.percontig.tsv") into taxo_percontig_ch