Clean ESMFold outputs | --env flags for apptainer enginer

CHANGELOG.md

@@ -92,6 +92,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Add `boltz_use_kernels` parameter to enable/disable using optimized Triton-based CUDA kernels CUDA kernels for Boltz inference.
 - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Handle incompatible CUDA kernel errors in Boltz by automatically retrying with `--no_kernels` false.
 - [[PR #454](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for alphafold2 modules
+- [[PR #464](https://github.com/nf-core/proteinfold/pulls/464)] - Update module conf and publishdir patterns for ESMFold, pass through container args
 
 ### Parameters
 

conf/modules_esmfold.config

@@ -12,19 +12,19 @@
 
 process {
     withName: 'RUN_ESMFOLD' {
-        ext.args = {params.use_gpu ? '' : '--cpu-only'}
+        ext.args = ''
+        containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp'
         publishDir = [
             [
-                path: { "${params.outdir}/esmfold/default" },
+                path: { "${params.outdir}/esmfold/${meta.id}" },
                 mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                pattern: '*.*'
+                pattern: '*_plddt.tsv'
             ],
             [
-                path: { "${params.outdir}/esmfold/default/top_ranked_structures" },
+                path: { "${params.outdir}/esmfold/top_ranked_structures" },
                 mode: 'copy',
                 saveAs: { "${meta.id}.pdb" },
-                pattern: '*.pdb'
+                pattern: '*_esmfold.pdb'
             ]
         ]
     }