Merge branch '13-add.flowcell.to.outputs' into 'develop'

Resolve "Handle multi-flowcells in fastqc and multiqc"

Closes #13

See merge request !18

workflow/conf/biohpc.config

@@ -20,7 +20,7 @@ process {
     executor = 'super'
   }
   withLabel:versions {
-    module = ['python/3.6.1-2-anaconda']
+    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
     executor = 'local'
   }
   withLabel:multiqc {

workflow/main.nf

@@ -4,7 +4,7 @@
 // Note - $baseDir is the location of this workflow file main.nf
 
 // Define Input variables
-params.name = "small"
+params.name = "run"
 params.bcl = "$baseDir/../test_data/*.tar.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
 params.outDir = "$baseDir/output"
@@ -53,7 +53,7 @@ process untarBCL {
 
   output:
 
-  file("*") into bclPaths
+  file("*") into bclPaths mode flatten
 
   script:
 
@@ -62,12 +62,13 @@ process untarBCL {
   ulimit -a
   name=`echo ${tar} | rev | cut -f1 -d '.' | rev`;
   if [ "\${name}" == "gz" ];
-  then tar -xvf ${tar} -I pigz;
-  else tar -xvf ${tar};
+  then tar -xvf $tar -I pigz;
+  else tar -xvf $tar;
   fi;
   """
 }
 
+
 process mkfastq {
   tag "${bcl.baseName}"
   queue '128GB,256GB,256GBv1,384GB'
@@ -76,46 +77,46 @@ process mkfastq {
 
   input:
 
-  val bcl from bclPaths
-  file designPaths
+  each bcl from bclPaths.collect()
+  file design from designPaths
 
   output:
 
   file("**/outs/**/*.fastq.gz") into fastqPaths
   file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
-  file("version*.txt") into versionPaths_mkfastq
+  val "${bcl.baseName}" into bclName
 
   script:
 
   """
   hostname
   ulimit -a
-  sh $baseDir/scripts/versions_mkfastq.sh
-  cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$designPaths -r \$SLURM_CPUS_ON_NODE  -p \$SLURM_CPUS_ON_NODE  -w \$SLURM_CPUS_ON_NODE 
+  cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$design -r \$SLURM_CPUS_ON_NODE  -p \$SLURM_CPUS_ON_NODE  -w \$SLURM_CPUS_ON_NODE 
   """
 }
 
-
 process fastqc {
-  tag "$name"
+  tag "$bclName"
   queue 'super'
-  publishDir "$outDir/misc/${task.process}/$name", mode: 'copy', pattern: "{*fastqc.zip}"
+  publishDir "$outDir/misc/${task.process}/$name/$bclName", mode: 'copy', pattern: "{*fastqc.zip}"
   module 'fastqc/0.11.5:parallel'
 
   input:
   file fastqPaths
+  val bclName
 
   output:
 
   file("*fastqc.zip") into fqcPaths
-  file("version*.txt") into versionPaths_fastqc
 
   script:
 
   """
   hostname
   ulimit -a
+  find *.fastq.gz -exec mv {} $bclName.{} \\;
   bash $baseDir/scripts/fastqc.sh
+  
   """
 }
 
@@ -123,13 +124,10 @@ process fastqc {
 process versions {
   tag "$name"
   publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
-  module 'python/3.6.1-2-anaconda'
+  module 'python/3.6.1-2-anaconda:cellranger/3.0.2:bcl2fastq/2.19.1:fastqc/0.11.5'
 
   input:
 
-  file versionPaths_mkfastq
-  file versionPaths_fastqc
-
   output:
 
   file("*.yaml") into yamlPaths
@@ -140,21 +138,22 @@ process versions {
   hostname
   ulimit -a
   echo $workflow.nextflow.version > version_nextflow.txt
+  sh $baseDir/scripts/versions_mkfastq.sh
+  bash $baseDir/scripts/versions_fastqc.sh
   python3 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions
   """
 }
 
-
 process multiqc {
   tag "$name"
   queue 'super'
-  publishDir "$outDir/${task.process}/$name", mode: 'copy'
+  publishDir "$outDir/${task.process}/$name", mode: 'copy', pattern: "{multiqc*}"
   module 'multiqc/1.7'
 
   input:
 
-  file bqcPaths
-  file fqcPaths
+  file bqc name "bqc/?/*" from bqcPaths.collect()
+  file fqc name "fqc/*" from fqcPaths.collect()
   file yamlPaths
 
   output:

workflow/scripts/fastqc.sh

@@ -5,4 +5,3 @@ find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j
 #for i in `ls *.fastq.gz`;
 #do echo "fastqc ${i}";
 #done | parallel -j `grep -c ^processor /proc/cpuinfo` --verbose;
-fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt  

workflow/scripts/versions_fastqc.sh

+#!/bin/bash
+
+fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt