Merge branch 'fpwork' into 'main'

Build first draft of the fix for the module error encountered.

See merge request !7

astrocyte_pkg.yml

@@ -81,8 +81,8 @@ workflow_modules:
 # Singularity supports different registries, please specify the protocol to use.
 # Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
 # container registry of BioHPC to save and manage your container images.
-workflow_containers:
-  - docker://git.biohpc.swmed.edu:5050/s219741/astrocyte-atac-source/atac:0.0.1
+#workflow_containers:
+#  - docker://git.biohpc.swmed.edu:5050/s219741/astrocyte-atac-source/atac:0.0.1
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

workflow/configs/biohpc.config

+/*
 singularity {
   enabled = true
   runOptions = ''
@@ -13,7 +14,7 @@ singularity {
   cacheDir = "$baseDir/images/singularity"    // Singularity images specified in `workflow_containers` of astrocyte_pkg.yml will be saved to 
                                               // this folder automatically, before running the workflow. The images will be renamed as
                                               // "NAME-TAG.img", e.g. ubuntu-latest.img, centos-centos8.img, r-4.1.1.img, etc.
-}
+}*/
 
 process {
     executor = 'slurm'

workflow/main.nf

@@ -29,8 +29,9 @@ process runSource {
     
     shell:
     '''
-    module load python/3.8.x-anaconda
-    module load openjdk/18
+    export PATH="/cm/shared/apps/openjdk/18/jdk-18/bin:/cm/shared/apps/python/3.8.x-anaconda/condabin:/cm/shared/apps/python/3.8.x-anaconda/bin:$PATH"
+    python --version > python_version.txt
+    java -version 2> java_version_before.txt
 
     # Enable the use of bash-specific conda commands in this shell.
     eval "$(conda shell.bash hook)"