diff --git a/workflow/main.nf b/workflow/main.nf index 7ebcf8035ecfd95091552ab9928c03fae85d27dc..682a70d1ef14d2ce282d8a5f12e5473270d29796 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -21,6 +21,7 @@ process runSource { publishDir "$baseDir/output", mode: 'copy' input: + file inputJson from inputJsonFile output: @@ -28,12 +29,12 @@ process runSource { shell: ''' - # Enable the use of bash-specific conda commands in this shell. - eval "$(conda shell.bash hook)" - module load python/3.8.x-anaconda module load openjdk/18 + # Enable the use of bash-specific conda commands in this shell. + eval "$(conda shell.bash hook)" + # Create a temporary conda environment for caper. conda create -y -c bioconda -c defaults -c conda-forge --name astrocyte-atac-caper python=3.8.18 # Activate and install caper.