Build branch main with version main (10d3b38)

Build pipeline: viash-hub.htrnaseq.main-77sg6

Source commit: 10d3b382d6

Source message: Add runner integration tests, revert ec0dd8b (#64)

target/nextflow/workflows/runner/.config.vsh.yaml

@@ -99,14 +99,6 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
-- name: "Annotation flags"
-  arguments:
-  - type: "boolean_true"
-    name: "--plain_output"
-    description: "Flag to indicate that the output should be stored directly under\
-      \ $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n"
-    info: null
-    direction: "input"
 - name: "Publish arguments"
   arguments:
   - type: "string"
@@ -135,6 +127,11 @@ resources:
   path: "_viash.yaml"
   dest: "_viash.yaml"
 description: "Runner for HT RNA-seq pipeline"
+test_resources:
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf"
 info: null
 status: "enabled"
 scope:
@@ -238,9 +235,9 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
   dependencies:
   - "target/nextflow/utils/listInputDir"
   - "target/nextflow/workflows/htrnaseq"

target/nextflow/workflows/runner/main.nf

@@ -3150,17 +3150,6 @@ meta = [
         }
       ]
     },
-    {
-      "name" : "Annotation flags",
-      "arguments" : [
-        {
-          "type" : "boolean_true",
-          "name" : "--plain_output",
-          "description" : "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
-          "direction" : "input"
-        }
-      ]
-    },
     {
       "name" : "Publish arguments",
       "arguments" : [
@@ -3202,6 +3191,14 @@ meta = [
     }
   ],
   "description" : "Runner for HT RNA-seq pipeline",
+  "test_resources" : [
+    {
+      "type" : "nextflow_script",
+      "path" : "test.nf",
+      "is_executable" : true,
+      "entrypoint" : "test_wf"
+    }
+  ],
   "status" : "enabled",
   "scope" : {
     "image" : "public",
@@ -3336,9 +3333,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3551,20 +3548,10 @@ workflow run_wf {
     results_publish_ch = grouped_with_params_list_ch
       | publish_results.run(
         fromState: { id, state ->
-          def project = (state.plain_output) ? id : "${state.project_id}"
-          def experiment = (state.plain_output) ? id : "${state.experiment_id}"
-          def id0 = "${project}/${experiment}"
-          def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}"
-          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}"
-
-          if (id == id2) {
-            println("Publising results to ${params.results_publish_dir}")
-          } else {
-            println("Publising results to ${params.results_publish_dir}/${id2}")
-          }
+          def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
+          println("Publising results to ${params.results_publish_dir}/${output_dir}")
 
           [
-            star_output: state.star_output,
             star_output: state.star_output,
             nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
             star_qc_metrics: state.star_qc_metrics,
@@ -3573,7 +3560,7 @@ workflow run_wf {
             p_data: state.p_data,
             html_report: state.html_report,
             run_params: state.run_params,
-            output: "${id2}"
+            output: output_dir.toString()
           ]
         },
         toState: { id, result, state -> state },
@@ -3604,19 +3591,12 @@ workflow run_wf {
       }
       | publish_fastqs.run(
         fromState: { id, state ->
-          def id0 = state.run_id
-          def id1 = (state.plain_output) ? id : "${id0}/${date}"
-          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}/${state.sample_id}"
-
-          if (id == id2) {
-            println("Publising fastqs to ${params.fastq_publish_dir}")
-          } else {
-            println("Publising fastqs to ${params.fastq_publish_dir}/${id2}")
-          }
+          def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
+          println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}")
 
           [
             input: state.fastq_output,
-            output: "${id2}",
+            output: output_dir.toString(),
           ]
         },
         toState: { id, result, state -> state },

target/nextflow/workflows/runner/nextflow_schema.json

@@ -85,19 +85,6 @@
         }
       }
     },
-    "annotation flags": {
-      "title": "Annotation flags",
-      "type": "object",
-      "description": "No description",
-      "properties": {
-        "plain_output": {
-          "type": "boolean",
-          "description": "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
-          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
-          "default": false
-        }
-      }
-    },
     "publish arguments": {
       "title": "Publish arguments",
       "type": "object",
@@ -135,9 +122,6 @@
     {
       "$ref": "#/$defs/metadata arguments"
     },
-    {
-      "$ref": "#/$defs/annotation flags"
-    },
     {
       "$ref": "#/$defs/publish arguments"
     },