Compute contig bed from idxstat file

main.nf

@@ -711,7 +711,6 @@ process rename_contigs_genes {
   set replicateId, file("${replicateId}.annotated.faa") into prokka_renamed_faa_ch
   set replicateId, file("${replicateId}.annotated.gff") into prokka_renamed_gff_ch, prokka_renamed_gff_ch2
   set replicateId, file("${replicateId}_prot.len") into contigs_length_ch
-  set replicateId, file("${replicateId}_contig.bed") into contigs_bed_ch
 
   when: ('04_structural_annot' in step || '05_alignment' in step || '06_func_annot' in step || '07_taxo_affi' in step || '08_binning' in step)
 
@@ -720,7 +719,6 @@ process rename_contigs_genes {
   grep "^gnl" ${assembly_file}/${replicateId}.gff > ${replicateId}_only_gnl.gff
   Rename_contigs_and_genes.py -f ${replicateId}_only_gnl.gff -faa ${assembly_file}/${replicateId}.faa -ffn ${assembly_file}/${replicateId}.ffn -fna ${assembly_file}/${replicateId}.fna -p ${replicateId} -oGFF ${replicateId}.annotated.gff -oFAA ${replicateId}.annotated.faa -oFFN ${replicateId}.annotated.ffn -oFNA ${replicateId}.annotated.fna
   samtools faidx ${replicateId}.annotated.faa; cut -f 1,2 ${replicateId}.annotated.faa.fai > ${replicateId}_prot.len
-  samtools faidx ${replicateId}.annotated.fna; awk 'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}' ${replicateId}.annotated.fna.fai > ${replicateId}_contig.bed
   """
 }
 prokka_renamed_faa_ch.into{prokka_renamed_faa_ch2;  prokka_renamed_faa_ch4}
@@ -738,6 +736,7 @@ process reads_alignment_on_contigs {
    output:
    set val(replicateId), file("${replicateId}.sort.bam"), file("${replicateId}.sort.bam.bai") into reads_assembly_ch, reads_assembly_ch_for_metabat2, reads_assembly_ch_for_depth
    set val(replicateId), file("${replicateId}.sort.bam.idxstats") into idxstats_ch
+   set val(replicateId), file("${replicateId}_contig.bed") into contigs_bed_ch
 
    when: ('05_alignment' in step || '06_func_annot' in step || '07_taxo_affi' in step || '08_binning' in step)
 
@@ -747,6 +746,7 @@ process reads_alignment_on_contigs {
    bwa mem ${fna_prokka} ${deduplicated_reads_R1} ${deduplicated_reads_R2} | samtools view -bS - | samtools sort - -o ${replicateId}.sort.bam
    samtools index ${replicateId}.sort.bam
    samtools idxstats ${replicateId}.sort.bam > ${replicateId}.sort.bam.idxstats
+   awk 'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}' ${replicateId}.sort.bam.idxstats > ${replicateId}_contig.bed
    """
 }