Moved out genebody_coverage into its own process

nf-core · Aug 28, 2017 · f6f6669 · f6f6669
1 parent 9b6342b
commit f6f6669
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Showing 2 changed files with 42 additions and 10 deletions.
diff --git a/conf/uppmax.config b/conf/uppmax.config
@@ -60,16 +60,22 @@ process {
   $hisat2_sortOutput {
     module = ['bioinfo-tools', 'samtools/1.3']
     cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
+    memory = { 24.GB * task.attempt }
     time = { 8.h * task.attempt }
   }
   $rseqc {
     module = ['bioinfo-tools', 'rseqc/2.6.1', 'samtools/1.3']
-    cpus = { 8 * task.attempt }
-    memory = { 32.GB * task.attempt }
-    time = { 7.h * task.attempt }
+    cpus = { 1 * task.attempt }
+    memory = { 24.GB * task.attempt }
+    time = { 4.h * task.attempt }
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }
+  $genebody_coverage {
+    module = ['bioinfo-tools', 'rseqc/2.6.1', 'samtools/1.3']
+    cpus = { 1 * task.attempt }
+    memory = { 32.GB * task.attempt }
+    time = { 8.h * task.attempt }
+  }
   $preseq {
     module = ['bioinfo-tools', 'preseq/0.1.0']
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }

diff --git a/main.nf b/main.nf
@@ -579,7 +579,7 @@ if(params.aligner == 'star'){
     star_aligned
         .filter { logs, bams -> check_log(logs) }
         .flatMap {  logs, bams -> bams }
-    .into { bam_count; bam_rseqc; bam_preseq; bam_markduplicates; bam_featurecounts; bam_stringtieFPKM }
+    .into { bam_count; bam_rseqc; bam_preseq; bam_markduplicates; bam_featurecounts; bam_stringtieFPKM; bam_geneBodyCoverage }
 }
 
 
@@ -656,7 +656,7 @@ if(params.aligner == 'hisat2'){
         file hisat2_bam
 
         output:
-        file "${hisat2_bam.baseName}.sorted.bam" into bam_count, bam_rseqc, bam_preseq, bam_markduplicates, bam_featurecounts, bam_stringtieFPKM
+        file "${hisat2_bam.baseName}.sorted.bam" into bam_count, bam_rseqc, bam_preseq, bam_markduplicates, bam_featurecounts, bam_stringtieFPKM, bam_geneBodyCoverage
 
         script:
         def avail_mem = task.memory == null ? '' : "-m ${task.memory.toBytes() / task.cpus}"
@@ -669,7 +669,8 @@ if(params.aligner == 'hisat2'){
     }
 }
 
-
+bed12
+.into { bed_rseqc; bed_genebody_coverage } 
 /*
  * STEP 4 - RSeQC analysis
  */
@@ -707,7 +708,7 @@ process rseqc {
 
     input:
     file bam_rseqc
-    file bed12 from bed12.collect()
+    file bed12 from bed_rseqc.collect()
 
     output:
     file "*.{txt,pdf,r,xls}" into rseqc_results
@@ -722,18 +723,42 @@ process rseqc {
     """
     samtools index $bam_rseqc
     infer_experiment.py -i $bam_rseqc -r $bed12 > ${bam_rseqc.baseName}.infer_experiment.txt
-    RPKM_saturation.py -i $bam_rseqc -r $bed12  $strandRule -o ${bam_rseqc.baseName}.RPKM_saturation
     junction_annotation.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12
     bam_stat.py -i $bam_rseqc 2> ${bam_rseqc.baseName}.bam_stat.txt
     junction_saturation.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12 2> ${bam_rseqc.baseName}.junction_annotation_log.txt
     inner_distance.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12
-    geneBody_coverage.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12
     read_distribution.py -i $bam_rseqc -r $bed12 > ${bam_rseqc.baseName}.read_distribution.txt
     read_duplication.py -i $bam_rseqc -o ${bam_rseqc.baseName}.read_duplication
     echo "Filename $bam_rseqc RseQC version: "\$(read_duplication.py --version)
     """
 }
 
+/*
+ * Step 4.1 Rseqc genebody_coverage
+ */
+process genebody_coverage {
+    tag "${bam_geneBodyCoverage.baseName - '.sorted'}" 
+       publishDir "${params.outdir}/rseqc" , mode: 'copy',
+        saveAs: {filename ->
+            else if (filename.indexOf("geneBodyCoverage.curves.pdf") > 0)       "geneBodyCoverage/$filename"
+            else if (filename.indexOf("geneBodyCoverage.r") > 0)                "geneBodyCoverage/rscripts/$filename"
+            else if (filename.indexOf("geneBodyCoverage.txt") > 0)              "geneBodyCoverage/data/$filename"
+            else "$filename"
+        }
+
+    input:
+    file bam_geneBodyCoverage
+    file bed12 from bed_genebody_coverage.collect()
+
+    output:
+
+    file "*.{txt,pdf,r,xls}" into genebody_coverage_results
+    script:
+    """
+    samtools index $bam_geneBodyCoverage
+    geneBody_coverage.py -i $bam_geneBodyCoverage -o ${bam_geneBodyCoverage.baseName}.rseqc -r $bed12
+    """
+}
 
 /*
  * STEP 5 - preseq analysis
@@ -974,6 +999,7 @@ process multiqc {
     file ('trimgalore/*') from trimgalore_results.collect()
     file ('alignment/*') from alignment_logs.collect()
     file ('rseqc/*') from rseqc_results.collect()
+    file ('rseqc/*') from genebody_coverage_results.collect()
     file ('preseq/*') from preseq_results.collect()
     file ('dupradar/*') from dupradar_results.collect()
     file ('featureCounts/*') from featureCounts_logs.collect()