RNAseq.nf : fix coverage normalization (as I did before for RibosomeProfiling.nf)

src/RNAseq.nf

@@ -462,7 +462,7 @@ rnaseqc ${gtf} ${bam[0]} -s ${file_id} ./ \
 /* HISAT2 POST_GENOMIC */
 /////////////////////////
 
-process hisat2_postGenomic {
+process hisat2_postgenome {
   tag "$file_id"
   publishDir "${params.output}/05_post_genome_hisat2/", mode: 'copy'
 
@@ -569,51 +569,105 @@ process fastqc_postgenome {
 /* Coverage */
 //////////////
 
-process coverage_postgenome {
+if (params.do_postgenome){
+        HISAT_ALIGNED_COV.join(POSTGENOME_ALIGNED_COV)
+                         .into{COVERAGE_MERGED_VALUES;COVERAGE_MERGED_BAM}
+
+        process calc_scalingFactor_with_postgenome{
          tag "$file_id"
- publishDir "${params.output}/07_coverage/", mode: 'copy'
 
          input:
- set file_id, file(bam) from HISAT_ALIGNED_COV
- set file_id_2, file(post_genome) from POSTGENOME_ALIGNED_COV
+         set file_id, file(genome), file(post_genome) from COVERAGE_MERGED_VALUES
 
          output:
- file "*.bigwig" into COVERAGE_OUTPUT
-
- when:
- params.do_postgenome
+         set file_id, env(genome), env(postgenome), env(factor) into COVERAGE_MERGED_FACTOR
 
          shell:
          '''
- genome=$(samtools view !{bam[0]} | awk '{print $1}' | sort | uniq | wc -l)
+         genome=$(samtools view !{genome[0]} | awk '{print $1}' | sort | uniq | wc -l)
          postgenome=$(samtools view !{post_genome[0]} | awk '{print $1}' | sort | uniq | wc -l)
          total=$(($genome + $postgenome))
          factor=$(awk -v c=$total 'BEGIN {print 1000000/c}')
- bamCoverage -p !{task.cpus} --binSize 1 -b !{bam[0]} -o !{file_id}_genome.bigwig
- bamCoverage -p !{task.cpus} --binSize 1 -b !{post_genome[0]} -o !{file_id}_postgenome.bigwig
          '''
         }
 
-process coverage {
+        COVERAGE_MERGED_FACTOR.join(COVERAGE_MERGED_BAM)
+                              .set{COVERAGE_MERGED_BIGWIG}
+
+        process coverage_with_postgenome{
          tag "$file_id"
          publishDir "${params.output}/07_coverage/", mode: 'copy'
 
          input:
- set file_id, file(bam) from HISAT_ALIGNED_COV_2
+         set file_id, val(genome), val(postgenome), val (factor),  file(genome_bam), file(post_genome_bam) from COVERAGE_MERGED_BIGWIG
 
          output:
- file "*.bigwig" into COVERAGE_OUTPUT_2
+         file "*.bigwig" into COVERAGE_OUTPUT
+         file "*.txt" into COVERAGE_LOG
+
+         shell:
+         '''
+         total=$((!{genome} + !{postgenome}))
+         echo "genome aligment : !{genome} counts" >> !{file_id}.txt
+         echo "postgenome aligment : !{postgenome} counts" >> !{file_id}.txt
+         echo "total counts : $total" >> !{file_id}.txt
+         echo "scaling factor : !{factor}" >> !{file_id}.txt
+         if [ !{genome} -gt 0 ]
+         then
+           bamCoverage -p !{task.cpus} --binSize 1  --scaleFactor !{factor} -b !{genome_bam[0]} -o !{file_id}_genome.bigwig
+         fi
+         if [ !{postgenome} -gt 0 ]
+         then
+           bamCoverage -p !{task.cpus} --binSize 1  --scaleFactor !{factor} -b !{post_genome_bam[0]} -o !{file_id}_postgenome.bigwig
+         fi
+         '''
+        }
+} else {
+        HISAT_ALIGNED_COV.into{COVERAGE_MERGED_VALUES;COVERAGE_MERGED_BAM}
+
+        process calc_scalingFactor{
+         tag "$file_id"
+
+         input:
+         set file_id, file(genome) from COVERAGE_MERGED_VALUES
+
+         output:
+         set file_id, env(genome), env(factor) into COVERAGE_MERGED_FACTOR
 
- when:
- params.do_postgenome==false
          shell:
          '''
- genome=$(samtools view !{bam[0]} | awk '{print $1} | sort | uniq | wc -l)
+         genome=$(samtools view !{genome[0]} | awk '{print $1}' | sort | uniq | wc -l)
          factor=$(awk -v c=$genome 'BEGIN {print 1000000/c}')
- bamCoverage -p !{task.cpus} --binSize 1 -b !{bam[0]} -o !{file_id}.bigwig
          '''
         }
 
+        COVERAGE_MERGED_FACTOR.join(COVERAGE_MERGED_BAM)
+                              .set{COVERAGE_MERGED_BIGWIG}
+
+
+        process coverage {
+         tag "$file_id"
+         publishDir "${params.output}/07_coverage/", mode: 'copy'
+
+         input:
+         set file_id, val(genome), val (factor),  file(genome_bam) from COVERAGE_MERGED_BIGWIG
+
+         output:
+         file "*.bigwig" into COVERAGE_OUTPUT
+         file "*.txt" into COVERAGE_LOG
+
+         shell:
+         '''
+         echo "genome aligment : !{genome} counts" >> !{file_id}.txt
+         echo "scaling factor : !{factor}" >> !{file_id}.txt
+         if [ !{genome} -gt 0 ]
+         then
+           bamCoverage -p !{task.cpus} --binSize 1  --scaleFactor !{factor} -b !{genome_bam[0]} -o !{file_id}_genome.bigwig
+         fi
+         '''
+        }
+}
+
 
 /////////////
 /* MultiQC */