Viash 0.8.x

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.7.5
+viash_version: 0.8.0
 
 source: src
 target: target

workflows/ingestion/demux/config.vsh.yaml → src/workflows/ingestion/demux/config.vsh.yaml

@@ -1,6 +1,6 @@
 functionality:
   name: demux
-  namespace: ingestion
+  namespace: workflows/ingestion
   description: |
     Convert `.bcl` files to `.fastq` files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.
   info:
@@ -24,13 +24,11 @@ functionality:
       description: ID of the sample.
       example: foo
     - name: "--input"
-      alternatives: [ "-i" ]
       type: file
       required: true
       description: Input run directory
       example: bcl_dir
     - name: "--sample_sheet"
-      alternatives: [ "-s" ]
       type: file
       required: true
       description: Pointer to the sample sheet
@@ -43,11 +41,38 @@ functionality:
     - name: "--ignore_missing"
       type: boolean
       description: Should the demultiplexer ignore missing entities (filter, ...)
+    - name: "--output_fastq"
+      type: file
+      direction: output
+      required: true
+      description: Output directory containig fastq files
+      example: fastq_dir
+    - name: "--output_fastqc"
+      type: file
+      direction: output
+      required: false
+      description: Reports directory produced by FastQC
+      example: reports_dir
+    - name: "--output_multiqc"
+      type: file
+      direction: output
+      required: false
+      description: Reports directory produced by MultiQC
+      example: reports_dir
   resources:
     - type: nextflow_script
       path: main.nf
+      entrypoint: run_wf
   test_resources:
     - type: nextflow_script
-      path: main.nf
+      path: test.nf
       entrypoint: test_wf
     - path: /resources_test/cellranger_tiny_bcl
+  dependencies:
+    - name: demux/cellranger_mkfastq
+    - name: demux/bcl_convert
+    - name: demux/bcl2fastq
+    - name: qc/fastqc
+    - name: qc/multiqc
+platforms:
+  - type: nextflow

workflows/ingestion/demux/integration_test.sh → src/workflows/ingestion/demux/integration_test.sh

@@ -12,7 +12,7 @@ export NXF_VER=21.10.6
 
 nextflow \
   run . \
-  -main-script workflows/ingestion/demux/main.nf \
+  -main-script src/workflows/ingestion/demux/test.nf \
   -entry test_wf \
   -resume \
   -profile docker,no_publish \

src/workflows/ingestion/demux/main.nf

@@ -0,0 +1,60 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    // translate the demultiplexer argument to the component name that needs to be run
+    | map { id, state ->
+      def funcNameMapper = [
+        bclconvert: "bcl_convert",
+        bcl2fastq: "bcl2fastq",
+        mkfastq: "cellranger_mkfastq"
+      ]
+      def funcName = funcNameMapper[state.demultiplexer]
+      def newState = state + [funcName: funcName]
+      [id, newState]
+    }
+
+    // run the demultiplexers
+    | runComponents(
+      components: [cellranger_mkfastq, bcl_convert, bcl2fastq],
+      filter: { id, state, config ->
+        state.funcName == config.functionality.name
+      },
+      fromState: { id, state, config ->
+        def data = [
+          input: state.input,
+          sample_sheet: state.sample_sheet,
+          reports: null // disable reports so they end up in the output dir
+        ]
+        if (config.functionality.name == "bcl2fastq") {
+          data.ignore_missing = state.ignore_missing
+        }
+        data
+      },
+      toState: ["output_fastq": "output"]
+    )
+
+    // run fastqc
+    | fastqc.run(
+      fromState: ["input": "output_fastq"],
+      args: [mode: "dir"],
+      toState: ["output_fastqc": "output"]
+    )
+
+    // run multiqc
+    | multiqc.run(
+      fromState: { id, state ->
+        ["input": [state.output_fastq]]
+      },
+      toState: ["output_multiqc": "output"]
+    )
+
+    // subset state to the outputs
+    | setState(["output_fastq", "output_fastqc", "output_multiqc"])
+
+  emit:
+  output_ch
+}

workflows/ingestion/demux/nextflow.config → src/workflows/ingestion/demux/nextflow.config

@@ -3,7 +3,7 @@ manifest {
 }
 
 params {
-  rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString()
+  rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString()
 }
 
 // include common settings

src/workflows/ingestion/demux/test.nf

@@ -0,0 +1,57 @@
+nextflow.enable.dsl=2
+
+// TODO: once viash supports 'viash test' on this workflow,
+//   - the import will be added automatically
+//   - access the test resources with `meta.resources_dir' instead of `params.resources_test'
+
+include { demux } from params.rootDir + "/target/nextflow/workflows/ingestion/demux/main.nf"
+
+workflow test_wf {
+  // TODO: change this to `resources_test = meta.resources_dir`
+  resources_test = file("${params.rootDir}/resources_test")
+
+  // or when running from s3:
+  Channel.fromList([
+    [
+      id: "mkfastq_test",
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
+      demultiplexer: "mkfastq"
+    ],
+    [
+      id: "bclconvert_test",
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl2/"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl2/sample_sheet.csv"),
+      demultiplexer: "bclconvert"
+    ],
+    [
+      id: "bcl2fastq_test",
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
+      demultiplexer: "bcl2fastq",
+      ignore_missing: true
+    ]
+  ])
+    | map{ state -> [state.id, state] }
+    | demux
+    | view { output ->
+      assert output.size() == 2 : "outputs should contain two elements; [id, state]"
+
+      def id = output[0]
+      assert id.contains("_test")
+
+      def state = output[1]
+      assert state.containsKey("output_fastq") : "State should contain output_fastq"
+      assert state.output_fastq.isDirectory() : "output_fastq should be a directory."
+      assert state.containsKey("output_fastqc") : "State should contain output_fastqc"
+      assert state.output_fastqc.isDirectory() : "output_fastqc should be a directory."
+      assert state.containsKey("output_multiqc") : "State should contain output_multiqc"
+      assert state.output_multiqc.isDirectory() : "output_multiqc should be a directory."
+
+      "Output: $output"
+    }
+    | toSortedList()
+    | map { output_list ->
+      assert output_list.size() == 3 : "There should be three outputs"
+    }
+}