Merge remote-tracking branch 'origin/main' into release

Author: rcannood

.gitignore

@@ -30,6 +30,4 @@ log.txt
 out/
 output/
 output_log/
-resources/test/
-resources_test/
-old_resources
+resources_test

workflows/1_ingestion/bd_rhapsody_wta/nextflow.config

@@ -17,7 +17,7 @@ includeConfig "$targetDir/transfer/publish/nextflow.config"
 // END INSERT
 
 docker {
-  runOptions = "-v $rootDir:$rootDir -v $viash_temp:$viash_temp"
+  runOptions = "-v ${params.rootDir}:${params.rootDir} -v $viash_temp:$viash_temp"
 }
 
 process {

workflows/2_single_modality/tx_processing/nextflow.config

@@ -27,7 +27,7 @@ includeConfig "$targetDir/transfer/publish/nextflow.config"
 // END INSERT
 
 docker {
-  runOptions = "-v $rootDir:$rootDir -v $viash_temp:$viash_temp"
+  runOptions = "-v ${params.rootDir}:${params.rootDir} -v $viash_temp:$viash_temp"
 }
 
 process {