Merge pull request #818 from nf-core/optional-ulimit

Provide users the ability to not bump stack size.

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#818](https://github.com/nf-core/ampliseq/pull/818) - Provide users the ability to not bump stack size in vsearch clustering.
+
 ### `Fixed`
 
 - [#800](https://github.com/nf-core/ampliseq/pull/800) - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF

modules/local/filter_clusters.nf

@@ -23,8 +23,9 @@ process FILTER_CLUSTERS {
     script:
     def prefix   = task.ext.prefix ?: "'$meta.id'"
     def clusters = "'$clusters'"
+    def ulimiter = params.raise_filter_stacksize ? "ulimit -s unlimited" : ""
     """
-    ulimit -s unlimited
+    ${ulimiter}
     echo ${clusters} | filt_clusters.py -t ${asv} -p ${prefix} -c -
 
     cat <<-END_VERSIONS > versions.yml

nextflow.config

@@ -82,6 +82,7 @@ params {
     ancombc_significance       = 0.05
     ancombc_formula            = null
     ancombc_formula_reflvl     = null
+    raise_filter_stacksize     = true
 
     // Report options
     report_template   = "${projectDir}/assets/report_template.Rmd"

nextflow_schema.json

@@ -288,6 +288,13 @@
                     "description": "Pairwise Identity value used when post-clustering ASVs if `--vsearch_cluster` option is used (default: 0.97).",
                     "help_text": "Lowering or increasing this value can change the number ASVs left over after clustering."
                 },
+                "raise_filter_stacksize": {
+                    "type": "boolean",
+                    "default": true,
+                    "fa_icon": "fas fa-angle-double-up",
+                    "description": "Raise stack size when filtering VSEARCH clusters",
+                    "help_text": "Setting to true adds 'ulimit -s unlimited' to the beginning of the filt_clusters.py command."
+                },
                 "filter_ssu": {
                     "type": "string",
                     "description": "Enable SSU filtering. Comma separated list of kingdoms (domains) in Barrnap, a combination (or one) of \"bac\", \"arc\", \"mito\", and \"euk\". ASVs that have their lowest evalue in that kingdoms are kept.",