feat(katana): Added katana config

Australian-Structural-Biology-Computing · Sep 5, 2024 · 5fe8e1d · 5fe8e1d
1 parent 0795469
commit 5fe8e1d
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf
@@ -9,7 +9,6 @@ process RUN_ALPHAFOLD2_PRED {
         'docker://nfcore/proteinfold_alphafold2_split:1.0.0' :
         'nfcore/proteinfold_alphafold2_split:1.0.0' }"
     echo 'true'
-
     input:
     tuple val(meta), path(fasta)
     val   db_preset
@@ -38,9 +37,10 @@ process RUN_ALPHAFOLD2_PRED {
     def args = task.ext.args ?: ''
     """
     echo \$PWD
-    if [ -d ${params.alphafold2_db}/${params.alphafold2_params_path} ]; 
-        then ln -r -s params/alphafold_params_*/* params/
-    fi
+    #if [ -d ${params.alphafold2_params_path} ]; 
+    #then
+    ln -r -f -s ${params.alphafold2_params_path}* params/
+    #fi
     python3 /app/alphafold/run_predict.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \

diff --git a/nextflow.config b/nextflow.config
@@ -146,8 +146,10 @@ params {
 
 }
 
+spack.enabled = true
+
 // Load base.config by default for all pipelines
-includeConfig 'conf/base.config'
+includeConfig 'conf/katana.config'
 
 // Load nf-core custom profiles from different Institutions
 try {

diff --git a/pf_files/proteinfold_test.sh b/pf_files/proteinfold_test.sh
@@ -1,4 +1,4 @@
-module load nextflow/23.04.4 java/11
+module load nextflow/23.04.4 java/11 cuda/11.8.0
 
 export SINGULARITY_CACHE_DIR=/srv/scratch/$USER/Singularity/cache
 export NXF_SINGULARITY_CACHEDIR=/srv/scratch/$USER/Singularity/cache