Use shared Nextflow container env vars

Author: jscgh

.env.example

@@ -9,8 +9,8 @@ PFOLD_NATIVE_GPU="-l select=1:ncpus=8:ngpus=1:mem=124gb;-l walltime=12:00:00"
 PFOLD_RUN_ENVIRONMENT=prod
 PFOLD_PROJECT_ROOT=/path/to/proteinfold
 PFOLD_DB_PATH=/path/to/proteinfold/dbs
-PFOLD_BRANCH=master
-PFOLD_REPOSITORY=Australian-Structural-Biology-Computing/proteinfold
+PFOLD_BRANCH=2.0.0
+PFOLD_REPOSITORY=nf-core/proteinfold
 PFOLD_NEXTFLOW_CONFIG=/path/to/proteinfold/nextflow.config
 
 # Runtime directories
@@ -22,7 +22,7 @@ PFOLD_DEBUGGROUP=your_group
 # Container caches
 APPTAINER_CACHEDIR=/path/to/cache/apptainer
 SINGULARITY_CACHEDIR=/path/to/cache/singularity
-PFOLD_NXF_APPTAINER_CACHEDIR=/path/to/cache/apptainer
-PFOLD_NXF_SINGULARITY_CACHEDIR=/path/to/cache/singularity
-PFOLD_NXF_APPTAINER_LIBRARYDIR=/path/to/library/apptainer
-PFOLD_NXF_SINGULARITY_LIBRARYDIR=/path/to/library/singularity
+NXF_APPTAINER_CACHEDIR=/path/to/cache/apptainer
+NXF_SINGULARITY_CACHEDIR=/path/to/cache/singularity
+NXF_APPTAINER_LIBRARYDIR=/path/to/library/apptainer
+NXF_SINGULARITY_LIBRARYDIR=/path/to/library/singularity

template/script.sh.erb

@@ -27,10 +27,10 @@ require_var PFOLD_BASE_NXF_WORK
 require_var PFOLD_BASE_OUT_DIR
 require_var APPTAINER_CACHEDIR
 require_var SINGULARITY_CACHEDIR
-require_var PFOLD_NXF_APPTAINER_CACHEDIR
-require_var PFOLD_NXF_SINGULARITY_CACHEDIR
-require_var PFOLD_NXF_APPTAINER_LIBRARYDIR
-require_var PFOLD_NXF_SINGULARITY_LIBRARYDIR
+require_var NXF_APPTAINER_CACHEDIR
+require_var NXF_SINGULARITY_CACHEDIR
+require_var NXF_APPTAINER_LIBRARYDIR
+require_var NXF_SINGULARITY_LIBRARYDIR
 
 RUN_ENVIRONMENT=${RUN_ENVIRONMENT:-${PFOLD_RUN_ENVIRONMENT}}
 PROJECT_ROOT=${PROJECT_ROOT:-${PFOLD_PROJECT_ROOT}}
@@ -82,10 +82,10 @@ export APPTAINER_CACHEDIR="${APPTAINER_CACHEDIR}"
 export SINGULARITY_CACHEDIR="${SINGULARITY_CACHEDIR}"
 
 # Nextflow variables, checks libraryDir and if image is not found downloads to cache
-export NXF_APPTAINER_CACHEDIR="${NXF_APPTAINER_CACHEDIR:-${PFOLD_NXF_APPTAINER_CACHEDIR}}"
-export NXF_SINGULARITY_CACHEDIR="${NXF_SINGULARITY_CACHEDIR:-${PFOLD_NXF_SINGULARITY_CACHEDIR}}"
-export NXF_APPTAINER_LIBRARYDIR="${NXF_APPTAINER_LIBRARYDIR:-${PFOLD_NXF_APPTAINER_LIBRARYDIR}}"
-export NXF_SINGULARITY_LIBRARYDIR="${NXF_SINGULARITY_LIBRARYDIR:-${PFOLD_NXF_SINGULARITY_LIBRARYDIR}}"
+export NXF_APPTAINER_CACHEDIR="${NXF_APPTAINER_CACHEDIR}"
+export NXF_SINGULARITY_CACHEDIR="${NXF_SINGULARITY_CACHEDIR}"
+export NXF_APPTAINER_LIBRARYDIR="${NXF_APPTAINER_LIBRARYDIR}"
+export NXF_SINGULARITY_LIBRARYDIR="${NXF_SINGULARITY_LIBRARYDIR}"
 
 export PROTEINFOLD_VERSION="2.0.0dev"