bind mounts moved to process directives

LANL-Bioinformatics · Jan 8, 2025 · 17f1894 · 17f1894
1 parent 6100ec0
commit 17f1894
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Showing 3 changed files with 15 additions and 6 deletions.
diff --git a/workflows/Nextflow/modules/contigsTaxonomyAssignment/contigsTaxonomyAssignment.nf b/workflows/Nextflow/modules/contigsTaxonomyAssignment/contigsTaxonomyAssignment.nf
@@ -5,10 +5,13 @@
 //base process. Takes a FASTA file containing contigs and performs taxonomic analysis with MICCR (https://github.com/chienchi/miccr).
 process contigTaxonomy {
     label 'cta'
+    containerOptions "--compat --cleanenv --home \
+                        --bind /media/volume/sdb/nextflow/database/miccrDB:/venv/database/miccrDB"
     publishDir(
         path: "${settings["outDir"]}/AssemblyBasedAnalysis/Taxonomy",
         mode: 'copy'
     )
+
     input:
     val settings
     path contigs
@@ -31,6 +34,8 @@ process contigTaxonomy {
 //adds multi-level taxonomic classification to results file. Takes in a .ctg.tsv file produced by MICCR.
 process addLineage {
     label 'cta'
+    containerOptions "--compat --cleanenv --home \
+                        --bind /media/volume/sdb/nextflow/database/miccrDB:/venv/database/miccrDB"
     publishDir(
         path: "${settings["outDir"]}/AssemblyBasedAnalysis/Taxonomy",
         mode: 'copy'

diff --git a/workflows/Nextflow/modules/readsTaxonomyAssignment/readsTaxonomyAssignment.nf b/workflows/Nextflow/modules/readsTaxonomyAssignment/readsTaxonomyAssignment.nf
@@ -3,6 +3,11 @@
 //main RTA process
 process readsTaxonomy {
     label 'rta'
+
+    containerOptions "--compat --cleanenv --home \
+                        --bind /media/volume/sdd/nextflow/database:/venv/bin/../../../database \
+                        --bind /media/volume/sdd/nextflow/krona_dbs:/venv/opt/krona/taxonomy"
+
     publishDir(
         path: "${settings["outDir"]}/ReadsBasedAnalysis/Taxonomy",
 	mode: 'copy',
@@ -43,6 +48,10 @@ process readsTaxonomy {
 process readsTaxonomyConfig {
     label 'rta'
 
+    containerOptions "--compat --cleanenv --home \
+                        --bind /media/volume/sdd/nextflow/database:/venv/bin/../../../database \
+                        --bind /media/volume/sdd/nextflow/krona_dbs:/venv/opt/krona/taxonomy"
+
     input:
     val settings
     val avgLen

diff --git a/workflows/Nextflow/nextflow.config b/workflows/Nextflow/nextflow.config
@@ -133,12 +133,7 @@ params {
 apptainer {
     enabled = true
     pullTimeout = "1 hour"
-    //binds are installation-dependent binds to databases
-    //not all bound paths are accessed by all containers
-    runOptions = "--compat --cleanenv --home /media/volume/sdd/nextflow \
-                    --bind /media/volume/sdd/nextflow/database:/venv/bin/../../../database \
-                    --bind /media/volume/sdd/nextflow/krona_dbs:/venv/opt/krona/taxonomy \
-                    --bind /media/volume/sdb/nextflow/database/miccrDB:/venv/database/miccrDB"
+    runOptions = "--compat --cleanenv --home"
 }