ensure cascadia can work in apptainer

Author: mriffle

container_images.config

@@ -9,7 +9,7 @@ params {
         encyclopedia3_mriffle: 'quay.io/protio/encyclopedia:3.0.0-MRIFFLE',
         qc_pipeline:           'quay.io/mauraisa/dia_qc_report:2.3.1',
         proteowizard:          'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.24172-63d00b1',
-        cascadia:              'quay.io/protio/cascadia:0.0.7',
+        cascadia:              'quay.io/protio/cascadia:0.0.8',
         cascadia_utils:        'quay.io/protio/cascadia-utils:0.0.4'
     ]
 }

modules/cascadia.nf

@@ -20,6 +20,9 @@ process CASCADIA_SEARCH {
     // don't melt the GPU
     maxForks params.cascadia.use_gpu ? 1 : null
 
+    // add extra command for apptainer
+    def extra_command = workflow.containerEngine in ['apptainer','singularity'] ? 'source /usr/local/bin/entrypoint.sh' : ''
+
     input:
         path ms_file
 
@@ -34,6 +37,7 @@ process CASCADIA_SEARCH {
     script:
 
         """
+        ${extra_command}
         cascadia sequence ${ms_file} /usr/local/bin/cascadia.ckpt --out ${ms_file.baseName}
             > >(tee "${ms_file.baseName}.stdout") 2> >(tee "${ms_file.baseName}.stderr" >&2)