Stub

.github/workflows/ci.yml

@@ -43,4 +43,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -stub

conf/modules.config

@@ -63,6 +63,7 @@ process {
             '--merged',
             '--exclude_predicted',
             '--fields "SYMBOL,Gene"',
+            '--transcript_filter "stable_id match ENST"'
         ].join(' ').trim()}
     }
 }

modules/local/exomedepth/cnv_call/main.nf

@@ -35,4 +35,16 @@ process CNV_CALL {
         R: \$(Rscript --version | sed 's/R scripting front-end //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${sample}_CNVs_ExomeDepth_${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ExomeDepth: ${VERSION}
+        R: \$(Rscript --version | sed 's/R scripting front-end //g')
+    END_VERSIONS
+    """
 }

modules/local/exomedepth/count/main.nf

@@ -39,4 +39,15 @@ process COUNT {
     END_VERSIONS
 
     """
+
+    stub:
+    """
+    touch ${meta.id}_${meta2.id}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ExomeDepth: ${VERSION}
+        R: \$(Rscript --version | sed 's/R scripting front-end //g')
+    END_VERSIONS
+    """
 }

modules/local/exomedepth/merge_cnv/main.nf

@@ -17,4 +17,9 @@ process CNV_MERGE {
     tail +2 $chrx >> "${prefix}.txt"
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta}_CNVs_ExomeDepth"
+    """
+    touch ${prefix}.txt
+    """
 }

modules/local/exomedepth/merge_count/main.nf

@@ -22,4 +22,10 @@ process COUNT_MERGE {
         fi
     done
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}_${meta.chr}"
+    """
+    touch ${prefix}.txt
+    """
 }

nextflow_schema.json

@@ -287,10 +287,6 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
-                "yamlconfig": {
-                    "type": "string",
-                    "description": "YAML config file to use in BEDGOVCF module"
                 }
             }
         },
@@ -300,6 +296,10 @@
             "description": "Options specific for the ExomeDepth execution",
             "default": "",
             "properties": {
+                "yamlconfig": {
+                    "type": "string",
+                    "description": "YAML config file to use in BEDGOVCF module"
+                },
                 "roi_auto": {
                     "type": "string",
                     "description": "Path to the default ROI (regions of interest) BED file of autosomal (merged) regions to be used for CNV analysis",