diff --git a/pfr/params.json b/pfr/params.json index e0e5e3e..5314052 100644 --- a/pfr/params.json +++ b/pfr/params.json @@ -3,8 +3,8 @@ "protein_evidence": "/workspace/genepal/testdata/0.4.0/external-protein-fastas.txt", "eggnogmapper_db_dir": "/workspace/ComparativeDataSources/emapperdb/5.0.2", "eggnogmapper_tax_scope": 33090, - "rna_evidence": "/workspace/genepal/testdata/0.4.0/fastqsheet.csv", + "rna_evidence": "/workspace/genepal/testdata/0.4.0/rnasheet.csv", "liftoff_annotations": "/workspace/genepal/testdata/0.4.0/liftoffannotations.csv", - "outdir": "results", - "busco_lineage_datasets": "embryophyta_odb10" + "busco_lineage_datasets": "embryophyta_odb10", + "outdir": "results" } diff --git a/pfr_genepal b/pfr_genepal index 3da5a74..d4f0fca 100644 --- a/pfr_genepal +++ b/pfr_genepal @@ -26,9 +26,8 @@ while getopts "t" opt; do done shift $((OPTIND -1)) -ml unload perl ml apptainer/1.1 -ml nextflow/23.04.4 +ml nextflow/24.04.3 export TMPDIR="/workspace/$USER/tmp" export APPTAINER_BINDPATH="$APPTAINER_BINDPATH,$TMPDIR:$TMPDIR,$TMPDIR:/tmp" @@ -38,7 +37,8 @@ if [ $full_test_flag -eq 1 ]; then main.nf \ -c pfr/profile.config \ -profile pfr,apptainer,test_full \ - -resume + -resume \ + --outdir results else nextflow \ main.nf \