src/RNAseq.nf : adapt hisat2 mapping

src/RNAseq.nf

@@ -7,11 +7,13 @@ params.output = "results"
 params.do_fastqc = true
 params.script_cov = "src/norm_coverage.sh"
 params.filter = "data/filter/human_rRNA_tRNA/*.bt2"
+params.index_genome = "data/genome/*.ht2"
 
 log.info "input raw : ${params.fastq_raw}"
 log.info "outut directory : ${params.output}"
 log.info "do fastqc ? : ${params.do_fastqc}"
 log.info "filter index files : ${params.filter}"
+log.info "genome index : ${params.index_genome}"
 
 Channel
    .fromFilePairs(params.fastq_raw)
@@ -24,6 +26,11 @@ Channel
    .ifEmpty { error "Cannot find any index files matching: ${params.filter}" }
    .set { FILTER_INDEX }
 
+Channel
+   .fromPath ( params.index_genome )
+   .ifEmpty { error "Cannot find any index files matching: ${params.index_genome}" }
+   .set { GENOME_INDEX }
+
 /* Fastqc of raw input */
 
 process fastqc_raw {
@@ -164,31 +171,20 @@ process fastqc_filter {
     """
 }
 
-/*	mapping against human genome with hisat2
-
-params.index_hg38 = "/media/adminmanu/Stockage/HISAT2_index_hg38_tran/*.ht2"
-
-log.info "index : ${params.index_hg38}"
-
-
-Channel
-  .fromPath ( params.index_hg38 )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index_hg38}" }
-  .set { index_file_hg38 }
+/*	mapping against human genome with hisat2 */
 
 process hisat2_human {
   tag "$file_id"
   publishDir "${params.output}/03_hisat2/", mode: 'copy'
-  errorStrategy 'finish'
 
   input:
-    set file_id, file(fastq_filtred) from rRNA_removed_files
-    file index from index_file_hg38.toList()
+    set file_id, file(fastq_filtred) from FILTER_FASTQ_HISAT
+    file index from GENOME_INDEX.toList()
 
   output:
-    file "*.fastq.gz" into reads_non_aligned_hg38
-    set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files
-    file "*.txt" into hisat_report
+    file "*.fastq.gz" into HISAT_UNALIGNED
+    set file_id, "*_sorted.{bam,bam.bai}" into HISAT_ALIGNED
+    file "*.txt" into HISAT_LOG
 
   script:
   index_id = index[0]
@@ -198,22 +194,24 @@ process hisat2_human {
     }
   }
 """
-hisat2 -x ${index_id} -p ${task.cpus} \
--1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} \
+hisat2 -x ${index_id} \
+       -p ${task.cpus} \
+       -1 ${fastq_filtred[0]} \
+       -2 ${fastq_filtred[1]} \
        --un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
---rna-strandness 'F' 2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
+       --rna-strandness 'F' \
+       2> ${file_id}_hisat2_hg38.txt \
+| samtools view -bS -F 4 - \
+| samtools sort -@ ${task.cpus} -o ${file_id}.bam \
+&& samtools index ${file_id}.bam
 
 if grep -q "ERR" ${file_id}_hisat2_hg38.txt; then
   exit 1
 fi
-
-samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${file_id}.bam
-samtools index ${file_id}_sorted.bam
-
 """
 }
 
-sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
+//sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
 
 /*                   HTseq