diff --git a/.gitignore b/.gitignore index 3749adb..46ee81c 100755 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ work *.nextflow* Sample_files .default_output +GRCh38.primary_assembly.genome.fa diff --git a/modules/processes.nf b/modules/processes.nf index 7b296c9..39e6708 100755 --- a/modules/processes.nf +++ b/modules/processes.nf @@ -28,7 +28,7 @@ process MINIMAP2_INDEX { process MINIMAP2_SAM { tag "$meta" - + memory { 4.GB * task.attempt } errorStrategy { task.attempt <= 5 ? "retry" : "finish" } maxRetries 5 @@ -44,7 +44,7 @@ process MINIMAP2_SAM { script: """ - minimap2 -ax map-ont -t 12 $index $reads > ${meta}.sam + minimap2 -ax map-ont -t $task.cpus $index $reads > ${meta}.sam cat <<-END_VERSIONS > versions.yml "${task.process}":