diff --git a/conf/base.config b/conf/base.config index c628a10c..c16be532 100644 --- a/conf/base.config +++ b/conf/base.config @@ -63,4 +63,9 @@ process { withName:CUSTOM_DUMPSOFTWAREVERSIONS { cache = false } + withName:QIIME2_EXTRACT { + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 24.h * task.attempt, 'time' ) } + } } diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index f3a61b6e..7ff383fd 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -1,7 +1,5 @@ process QIIME2_EXTRACT { tag "${meta.FW_primer}-${meta.RV_primer}" - label 'process_low' - label 'single_cpu' container "qiime2/core:2023.7" @@ -20,6 +18,7 @@ process QIIME2_EXTRACT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." } + def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="./xdgconfig" export MPLCONFIGDIR="./mplconfigdir" @@ -37,9 +36,11 @@ process QIIME2_EXTRACT { --output-path ref-taxonomy.qza #Extract sequences based on primers qiime feature-classifier extract-reads \\ + --p-n-jobs ${task.cpus} \\ --i-sequences ref-seq.qza \\ --p-f-primer ${meta.FW_primer} \\ --p-r-primer ${meta.RV_primer} \\ + $args \\ --o-reads ${meta.FW_primer}-${meta.RV_primer}-ref-seq.qza \\ --quiet