add coverage option in pipeline

src/RNAseq.config

@@ -57,10 +57,19 @@ profiles {
           clusterOptions = "-cwd -V"
           memory = "20GB"
           cpus = 16
-  	      penv = 'openmp16'
+  	  penv = 'openmp16'
+          time = "12h"
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+      }
+      withName: coverage {
+          container = "lbmc/deeptools:3.0.2"
+          executor = "sge"
+          clusterOptions = "-cwd -V"
+          memory = "20GB"
+          cpus = 16
+  	  penv = 'openmp16'
           time = "12h"
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
-          penv = 'openmp16'
       }
       withName: fastqc_genome {
           container = "lbmc/fastqc:0.11.5"
@@ -119,7 +128,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: rnaseq_qc {
-          container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:2.3.6"
+          module = "RNAseq-QC/2.3.6"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
@@ -193,8 +202,8 @@ profiles {
         container = "lbmc/multiqc:1.7"
         cpus = 1
       }
-      withName: coverage_genome {
-        container = "lbmc/deeptools:3.1.1"
+      withName: coverage {
+        container = "lbmc/deeptools:3.0.2"
         cpus = 8
       }
     }

src/RNAseq.nf

@@ -304,7 +304,8 @@ fi
 }
 
 HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC;
-                   HISAT_ALIGNED_DEDUP}
+                   HISAT_ALIGNED_DEDUP;
+                   HISAT_ALIGNED_COV}
 
 ////////////////////////////
 /* Fastqc of genome reads */
@@ -328,6 +329,27 @@ process fastqc_genome {
     """
 }
 
+
+//////////////
+/* Coverage */
+//////////////
+
+process coverage {
+ tag "$file_id"
+ publishDir "${params.output}/03_hisat2/coverage/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from HISAT_ALIGNED_COV
+
+ output:
+ file "*.bigwig" into COVERAGE_OUTPUT
+
+ """
+ bamCoverage -p ${task.cpus} --binSize 1 -b ${bam[0]} -o ${file_id}.bigwig
+
+ """
+}
+
 ////////////////////////////
 /* Deduplication of reads */
 ////////////////////////////

src/RibosomeProfiling.nf

@@ -291,7 +291,8 @@ fi
 }
 
 HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC;
-                   HISAT_ALIGNED_DEDUP}
+                   HISAT_ALIGNED_DEDUP;
+                   HISAT_ALIGNED_COV}
 
 ////////////////////////////
 /* Fastqc of genome reads */
@@ -315,6 +316,25 @@ process fastqc_genome {
     """
 }
 
+//////////////
+/* Coverage */
+//////////////
+
+process coverage {
+ tag "$file_id"
+ publishDir "${params.output}/03_hisat2/coverage/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from HISAT_ALIGNED_COV
+
+ output:
+ file "*.bigwig" into COVERAGE_OUTPUT
+
+ """
+ bamCoverage -p ${task.cpus} --binSize 1 -b ${bam[0]} -o ${file_id}.bigwig
+ """
+}
+
 ////////////////////////////
 /* Deduplication of reads */
 ////////////////////////////