activate multi-cpu use in QIIME2_EXTRACT

nf-core · Jan 11, 2024 · 70b2e01 · 70b2e01
1 parent 815e62b
commit 70b2e01
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git 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
@@ -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