Modif RNAseq_XGR.nf Add Samtools filters

src/RNAseq_XGR.nf

@@ -64,7 +64,7 @@ params.fastq = "${project}/fastq/*_{1,2}.fq.gz"
 params.gtf = ""
 params.fasta = ""
 params.idx = ""
-params.filter_bam = "-F 268 -f 1 -q 10"
+params.filter_bam_mapped = "-F 268 -f 1 -q 10"
 
 params.fastp_out = "$params.project/fastp/"
 params.star_mapping_fastq_out = "$params.project/STAR/"
@@ -109,7 +109,8 @@ include { index_with_gtf } from "./nf_modules/star/main_2.7.8a.nf"
 include { mapping_fastq } from "./nf_modules/star/main_2.7.8a.nf"
 include { mapping_withindex } from "./nf_modules/star/main_2.7.8a.nf"
 include { htseq_count } from "./nf_modules/htseq/main.nf"
-include { filter_bam } from "./nf_modules/samtools/main.nf"
+
+include { filter_bam_mapped } from "./nf_modules/samtools/main.nf"
 include { stats_bam } from "./nf_modules/samtools/main.nf"
 include { sort_bam } from "./nf_modules/samtools/main.nf"
 include { index_bam } from "./nf_modules/samtools/main.nf"
@@ -137,7 +138,7 @@ workflow {
     
     index_with_gtf(genome_file, gtf_file.collect())
     mapping_fastq(index_with_gtf.out.index.collect(), fastp.out.fastq)
-    
+    filter_bam_mapped(mapping_fastq.out.bam)
   }
   else {
     idx_genome = "${params.idx}"
@@ -146,10 +147,13 @@ workflow {
       .set { genome_indexed_input }
     genome_indexed_input.view()
     mapping_withindex(genome_indexed_input.collect(), fastp.out.fastq)
-    htseq_count(mapping_withindex.out.bam, gtf_file)
+    stats_bam(mapping_withindex.out.bam)
+    filter_bam_mapped(mapping_withindex.out.bam)
   }
 
-  htseq_count(mapping_fastq.out.bam, gtf_file)
+  sort_bam(filter_bam_mapped.out.bam)
+  index_bam(sort_bam_mapped.out.bam)
+  htseq_count(sort_bam_mapped.out.bam, gtf_file)
 
     //########################## QUALITY CHECKS ###################