diff --git a/workflow/main.nf b/workflow/main.nf index 9d5a92d3aa5cb071c4b0d093db20c28109058084..1f8219a58352ec4e682e739524e91e639ad57e06 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -36,7 +36,6 @@ references = params.references process checkDesignFile { tag "${name}" - module 'python/3.6.1-2-anaconda' input: file designLocation @@ -62,7 +61,6 @@ process checkDesignFile { process untarBCL { tag "${tar}" - module 'pigz/2.4' input: file tar from tarList @@ -83,9 +81,7 @@ process untarBCL { process mkfastq { tag "${bcl.baseName}" - queue '128GB,256GB,256GBv1,384GB' publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}" - module 'cellranger/3.1.0:bcl2fastq/2.19.1' input: each bcl from bclPaths.collect() @@ -134,8 +130,6 @@ if (bclCount.value == 1) { process fastqc { tag "${bclName}" - queue 'super' - module 'fastqc/0.11.5:parallel' input: file fastqPaths @@ -158,7 +152,6 @@ process fastqc { process versions { tag "${name}" - module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7' input: @@ -182,9 +175,7 @@ process versions { process multiqc { tag "${name}" - queue 'super' publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}" - module 'multiqc/1.7' input: file bqc name "bqc/?/*" from bqcPaths.collect()