Basic CI setup

workflow/main.nf

@@ -33,9 +33,6 @@ index_name = file(params.index).name
 // Output  - pair of fastq & generated sai file into the alignments channel 
 process bwa_aln {
 
-    // Tell Nextflow we will use 32 cpus here for BWA
-    cpus 32
-
     input:
     file fastq_file from fastqs
      
@@ -57,9 +54,6 @@ process bwa_aln {
 // Output  - .sam.gz into the samfiles channel, and baseDir/output
 process bwa_samse {
 
-    // bwa samse will use a single cpu core
-    cpus 1
-
     // Publish the outputs we create here into the workflow output directory
     publishDir "$baseDir/output", mode: 'copy'
     
@@ -86,10 +80,9 @@ process sam2bam {
 
 
     // Tell Nextflow picard will only use one cpu.
-    // We are allocating 32GB to java though, so tell
+    // We are allocating 16GB to java though, so tell
     // Nextflow so it can assign the task appropriately.
-    cpus 1
-    memory '32GB'
+    memory '16GB'
 
     // Publish the outputs we create here into the workflow output directory
     publishDir "$baseDir/output", mode: 'copy'
@@ -102,7 +95,7 @@ process sam2bam {
  
     """
     module add picard/1.127
-    java -Xmx32G -jar \$PICARD/picard.jar SortSam \
+    java -Xmx16G -jar \$PICARD/picard.jar SortSam \
     INPUT="${sam_file}" \
     OUTPUT="${sam_file.name}.bam" \
     SORT_ORDER=coordinate \