From 5fe8e1df99ff1df65575a5d0ae757f3f19a2e19b Mon Sep 17 00:00:00 2001 From: nbtm-sh Date: Thu, 5 Sep 2024 16:02:24 +1000 Subject: [PATCH] feat(katana): Added katana config --- modules/local/run_alphafold2_pred.nf | 8 ++++---- nextflow.config | 4 +++- pf_files/proteinfold_test.sh | 2 +- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf index cd7c93eb..9b371f86 100644 --- 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=${alphafold2_model_preset} \ diff --git a/nextflow.config b/nextflow.config index 691ee289..69cc7ad2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -146,8 +146,10 @@ params { } +spack.enabled = true + // Load base.config by default for all pipelines -includeConfig 'conf/base.config' +includeConfig 'conf/katana.config' // Load nf-core custom profiles from different Institutions try { diff --git a/pf_files/proteinfold_test.sh b/pf_files/proteinfold_test.sh index 3bdbc024..396a63f1 100755 --- a/pf_files/proteinfold_test.sh +++ b/pf_files/proteinfold_test.sh @@ -1,4 +1,4 @@ -module load nextflow/23.04.4 java/11 +module load nextflow/23.04.4 java/11 cuda/11.8.0 export SINGULARITY_CACHE_DIR=/srv/scratch/$USER/Singularity/cache export NXF_SINGULARITY_CACHEDIR=/srv/scratch/$USER/Singularity/cache