Build branch main with version main (60df288)

Build pipeline: viash-hub.htrnaseq.main-7kcqt

Source commit: 60df288f92

Source message: Replace ignore parameter with pools (#66)

target/nextflow/utils/listInputDir/.config.vsh.yaml

@@ -19,11 +19,9 @@ argument_groups:
     multiple: false
     multiple_sep: ";"
   - type: "string"
-    name: "--ignore"
-    description: "Pool names to ignore."
+    name: "--pools"
+    description: "Pool names to include. By default all pools are selected for analysis."
     info: null
-    default:
-    - "Undetermined"
     required: false
     direction: "input"
     multiple: true
@@ -171,9 +169,9 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "5a046ba00351f55ce8e9f524bc329dabda0a7a14"
+  git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-12-g5a046ba"
+  git_tag: "v0.7.2-13-g60df288"
 package_config:
   name: "htrnaseq"
   version: "main"

target/nextflow/utils/listInputDir/main.nf

@@ -3056,11 +3056,8 @@ meta = [
         },
         {
           "type" : "string",
-          "name" : "--ignore",
-          "description" : "Pool names to ignore.",
-          "default" : [
-            "Undetermined"
-          ],
+          "name" : "--pools",
+          "description" : "Pool names to include. By default all pools are selected for analysis.",
           "required" : false,
           "direction" : "input",
           "multiple" : true,
@@ -3239,9 +3236,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.4",
-    "git_commit" : "5a046ba00351f55ce8e9f524bc329dabda0a7a14",
+    "git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-12-g5a046ba"
+    "git_tag" : "v0.7.2-13-g60df288"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3320,7 +3317,7 @@ workflow run_wf {
           // Remove the trailing '_'
           def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "")
           def sample_id = parsedFastq[0][1]
-          if (sample_id in state.ignore) {
+          if (sample_id in ["Undetermined"] || (state.pools && !state.pools.isEmpty() && !state.pools.contains(sample_id))) {
             return null
           }
           return [

target/nextflow/utils/listInputDir/nextflow_schema.json

@@ -16,16 +16,13 @@
           "description": "Path to the directory containing fastq files",
           "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"fastq_dir\"`. "
         },
-        "ignore": {
+        "pools": {
           "type": "array",
           "items": {
             "type": "string"
           },
-          "description": "Pool names to ignore.",
-          "help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
-          "default": [
-            "Undetermined"
-          ]
+          "description": "Pool names to include",
+          "help_text": "Type: `string`, multiple: `True`. "
         },
         "r1_output": {
           "type": "string",