updated TrimGalore for multi-core support

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * Make executables in `bin/` compatible with Python 3
+* [#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
 
 ### `Dependencies`
 
@@ -36,6 +37,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Update homer `4.9.1` -> `4.10`
 * Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
 * Update bioconductor-vsn `3.46.0` -> `3.54.0`
+* Added pigz `2.3.4`
 
 ### `Deprecated`
 

environment.yml

@@ -18,6 +18,7 @@ dependencies:
   - conda-forge::r-lattice=0.20_38
   - conda-forge::r-upsetr=1.4.0
   - conda-forge::r-xfun=0.11
+  - conda-forge::pigz=2.3.4
   - r::r-stringi=1.4.3
 
   ## bioconda packages

main.nf

@@ -526,7 +526,7 @@ if (params.skip_trimming) {
 } else {
     process TrimGalore {
         tag "$name"
-        label 'process_long'
+        label 'process_medium'
         publishDir "${params.outdir}/trim_galore", mode: 'copy',
             saveAs: { filename ->
                           if (filename.endsWith(".html")) "fastqc/$filename"
@@ -553,13 +553,13 @@ if (params.skip_trimming) {
         if (params.single_end) {
             """
             [ ! -f  ${name}.fastq.gz ] && ln -s $reads ${name}.fastq.gz
-            trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq ${name}.fastq.gz
+            trim_galore -j $task.cpus --fastqc --gzip $c_r1 $tpc_r1 $nextseq ${name}.fastq.gz
             """
         } else {
             """
             [ ! -f  ${name}_1.fastq.gz ] && ln -s ${reads[0]} ${name}_1.fastq.gz
             [ ! -f  ${name}_2.fastq.gz ] && ln -s ${reads[1]} ${name}_2.fastq.gz
-            trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
+            trim_galore -j $task.cpus --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
             """
         }
     }