Fix TrimGalore core logic and update MultiQC

CHANGELOG.md

@@ -20,25 +20,27 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * Add genrich `0.6`
 * Add r-stringi `1.4.3`
+* Add pigz `2.3.4`
 * Update gawk `4.2.1` -> `5.0.1`
 * Update r-base `3.4.1` -> `3.6.1`
 * Update r-optparse `1.6.0` -> `1.6.4`
 * Update r-ggplot2 `3.1.0` -> `3.2.1`
 * Update r-pheatmap `1.0.10` -> `1.0.12`
 * Update r-lattice `0.20_35` -> `0.20_38`
 * Update r-upsetr `1.3.3` -> `1.4.0`
+* Update r-scales `1.0.0` -> `1.1.0`  
 * Update r-xfun `0.3` -> `0.11`
-* Update trim-galore `0.5.0` -> `0.6.4`
+* Update trim-galore `0.5.0` -> `0.6.5`
 * Update picard `2.19.0` -> `2.21.3`
 * Update pysam `0.15.2` -> `0.15.3`
 * Update bedtools `2.27.1` -> `2.29.0`
 * Update ucsc-bedgraphtobigwig `377` -> `357`
 * Update deeptools `3.2.1` -> `3.3.1`
 * Update macs2 `2.1.2` -> `2.2.5`
 * Update homer `4.9.1` -> `4.10`
+* Update multiqc `1.7` -> `1.8`
 * Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
 * Update bioconductor-vsn `3.46.0` -> `3.54.0`
-* Add pigz `2.3.4`
 
 ### `Deprecated`
 

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - conda-forge::r-rcolorbrewer=1.1_2
   - conda-forge::r-ggplot2=3.2.1
   - conda-forge::r-reshape2=1.4.3
-  - conda-forge::r-scales=1.0.0
+  - conda-forge::r-scales=1.1.0
   - conda-forge::r-pheatmap=1.0.12
   - conda-forge::r-lattice=0.20_38
   - conda-forge::r-upsetr=1.4.0
@@ -23,7 +23,7 @@ dependencies:
 
   ## bioconda packages
   - bioconda::fastqc=0.11.8
-  - bioconda::trim-galore=0.6.4
+  - bioconda::trim-galore=0.6.5
   - bioconda::bwa=0.7.17
   - bioconda::samtools=1.9
   - bioconda::picard=2.21.3
@@ -38,6 +38,6 @@ dependencies:
   - bioconda::ataqv=1.0.0
   - bioconda::subread=1.6.4
   - bioconda::preseq=2.0.3
-  - bioconda::multiqc=1.7
+  - bioconda::multiqc=1.8
   - bioconda::bioconductor-deseq2=1.26.0
   - bioconda::bioconductor-vsn=3.54.0

main.nf

@@ -526,7 +526,7 @@ if (params.skip_trimming) {
 } else {
     process TrimGalore {
         tag "$name"
-        label 'process_medium'
+        label 'process_high'
         publishDir "${params.outdir}/trim_galore", mode: 'copy',
             saveAs: { filename ->
                           if (filename.endsWith(".html")) "fastqc/$filename"
@@ -544,22 +544,36 @@ if (params.skip_trimming) {
         file "*.{zip,html}" into ch_trimgalore_fastqc_reports_mqc
 
         script:
+        // Calculate number of --cores for TrimGalore based on value of task.cpus
+        // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
+        // See: https://github.com/nf-core/atacseq/pull/65#issuecomment-557839116
+        def cores = 1
+        if (task.cpus) {
+            tcores = (((task.cpus as int) - 3) / 3) as int
+            if (tcores > 1) {
+                cores = tcores
+            }
+        }
+
+
         // Added soft-links to original fastqs for consistent naming in MultiQC
         c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
         c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
         tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
         tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
         nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
+
+        // Added soft-links to original fastqs for consistent naming in MultiQC
         if (params.single_end) {
             """
             [ ! -f  ${name}.fastq.gz ] && ln -s $reads ${name}.fastq.gz
-            trim_galore --cores $task.cpus --fastqc --gzip $c_r1 $tpc_r1 $nextseq ${name}.fastq.gz
+            trim_galore --cores $cores --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 --cores $task.cpus --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
+            trim_galore --cores $cores --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
             """
         }
     }