Build branch v0.3 with version v0.3.1 (35e1ab8)

Build pipeline: viash-hub.demultiplex.v0.3-jknqb

Source commit: 35e1ab8495

Source message: Bump version to 0.3.1

CHANGELOG.md

@@ -1,3 +1,15 @@
+# demultiplex v0.3.1
+
+# Minor updates
+
+* Add `--run_information` and `--demultiplexer` arguments to `runner` workflow (PR #27).
+
+# Bug fixes
+
+* Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).
+
+* Provide a clear error message when `--run_information` is provided but not `--demultiplexer` (PR #27).
+
 # demultiplex v0.3.0
 
 ## Major updates

_viash.yaml

@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.0
+version: v0.3.1
 description: |
   Demultiplexing pipeline
 license: MIT

src/dataflow/gather_fastqs_and_validate/main.nf

@@ -29,9 +29,9 @@ workflow run_wf {
               println "Encountered next header '[${start_parsing}]', stopping parsing."
               return true
             }
-            // [Data] for illumina
+            // [Data], [BCLConvert_Data] for illumina
             // [Samples] for Element Biosciences
-            if (header in ["Data", "Samples"]) {
+            if (header in ["Data", "Samples", "BCLConvert_Data"]) {
               println "Found header [${header}], start parsing."
               start_parsing = true
               return
@@ -56,7 +56,7 @@ workflow run_wf {
           return 
         }
         assert start_parsing: 
-          "Sample information file does not contain [Data] or [Samples] header!"
+          "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
         assert samples.size() > 1:
           "Sample information file does not seem to contain any information about the samples!"
         println "Finished processing run information file, found samples: ${samples}."

src/demultiplex/main.nf

@@ -25,6 +25,11 @@ workflow run_wf {
       | map {id, state ->
         def newState = [:]
         println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
+        // No auto-detection of run information file (it is user provided),
+        // in this case the demultiplexer should also be specified.
+        assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
+          "you must also provide a demultiplexer"
+
         if (!state.run_information) {
           println("Run information was not specified, auto-detecting...")
           // The supported_platforms hashmap must be a 1-on-1 mapping
@@ -62,7 +67,7 @@ workflow run_wf {
             "found in input directory."
 
           // When autodetecting, the demultiplexer must be set if the run information was found
-          assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
+          assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
             "Please report this as a bug."
 
           // When autodetecting, the found demultiplexer must match
@@ -82,7 +87,7 @@ workflow run_wf {
             "run_information": run_information,
             "demultiplexer": demultiplexer,
           ]
-        }
+        } // end auto-detection logic
 
         if (newState.demultiplexer in ["bclconvert"]) {
           // Do not add InterOp to state because we generate the summary csv's in the next

src/runner/config.vsh.yaml

@@ -7,6 +7,24 @@ argument_groups:
         description: Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/`
         type: file
         required: true
+      - name: --run_information
+        description: |
+          CSV file containing sample information, which will be used as 
+          input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)
+          or 'RunManifest.csv' (Element Biosciences). If not specified,
+          will try to autodetect the sample sheet in the input directory.
+          Requires --demultiplexer to be set.
+        type: file
+        required: false
+      - name: "--demultiplexer"
+        type: string
+        required: false
+        choices: ["bases2fastq", "bclconvert"]
+        description: |
+          Demultiplexer to use, choice depends on the provider
+          of the instrument that was used to generate the data.
+          When not using --sample_sheet, specifying this argument is not
+          required.
   - name: Annotation flags
     arguments:
       - name: --add_date_time

src/runner/main.nf

@@ -12,9 +12,11 @@ workflow run_wf {
       | demultiplex.run(
         fromState: [
           "input": "input",
+          "run_information": "run_information",
+          "demultiplexer": "demultiplexer",
           "output": "fastq",
           "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html",
+          "output_multiqc": "qc/multiqc_report.html"
         ],
         toState: { id, result, state ->
           state + result

target/executable/io/interop_summary_to_csv/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -141,12 +141,12 @@ build_info:
   output: "target/executable/io/interop_summary_to_csv"
   executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -160,7 +160,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# interop_summary_to_csv v0.3.0
+# interop_summary_to_csv v0.3.1
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.3.0"
+  echo "interop_summary_to_csv v0.3.1"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -470,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-12-11T09:19:38Z"
+LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.version="v0.3.1"
 
 VIASHDOCKER
   fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.3.0"
+            echo "interop_summary_to_csv v0.3.1"
             exit
             ;;
         --input)
@@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.1'
   fi
 
   # print dockerfile

target/executable/io/publish/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -170,12 +170,12 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish/publish

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish v0.3.0
+# publish v0.3.1
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.0"
+  echo "publish v0.3.1"
   echo ""
   echo "Publish the processed results of the run"
   echo ""
@@ -482,10 +482,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2024-12-11T09:19:38Z"
+LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.version="v0.3.1"
 
 VIASHDOCKER
   fi
@@ -621,7 +621,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish v0.3.0"
+            echo "publish v0.3.1"
             exit
             ;;
         --input)
@@ -778,7 +778,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.1'
   fi
 
   # print dockerfile

target/executable/io/untar/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -148,12 +148,12 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/untar/untar

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# untar v0.3.0
+# untar v0.3.1
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.0"
+  echo "untar v0.3.1"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -476,10 +476,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-12-11T09:19:39Z"
+LABEL org.opencontainers.image.created="2024-12-11T15:30:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+LABEL org.opencontainers.image.version="v0.3.1"
 
 VIASHDOCKER
   fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.3.0"
+            echo "untar v0.3.1"
             exit
             ;;
         --input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.1'
   fi
 
   # print dockerfile

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -139,12 +139,12 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -158,7 +158,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/combine_samples/main.nf

@@ -1,4 +1,4 @@
-// combine_samples v0.3.0
+// combine_samples v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_samples",
   "namespace" : "dataflow",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2972,13 +2972,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2995,7 +2995,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/dataflow/combine_samples/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/combine_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }
 

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -133,12 +133,12 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -152,7 +152,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.0
+// gather_fastqs_and_validate v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gather_fastqs_and_validate",
   "namespace" : "dataflow",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2965,13 +2965,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2988,7 +2988,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3042,9 +3042,9 @@ workflow run_wf {
               println "Encountered next header '[${start_parsing}]', stopping parsing."
               return true
             }
-            // [Data] for illumina
+            // [Data], [BCLConvert_Data] for illumina
             // [Samples] for Element Biosciences
-            if (header in ["Data", "Samples"]) {
+            if (header in ["Data", "Samples", "BCLConvert_Data"]) {
               println "Found header [${header}], start parsing."
               start_parsing = true
               return
@@ -3069,7 +3069,7 @@ workflow run_wf {
           return 
         }
         assert start_parsing: 
-          "Sample information file does not contain [Data] or [Samples] header!"
+          "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
         assert samples.size() > 1:
           "Sample information file does not seem to contain any information about the samples!"
         println "Finished processing run information file, found samples: ${samples}."

target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/gather_fastqs_and_validate'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }
 

target/nextflow/demultiplex/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -220,9 +220,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -234,7 +234,7 @@ build_info:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -248,7 +248,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/demultiplex/main.nf

@@ -1,4 +1,4 @@
-// demultiplex v0.3.0
+// demultiplex v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "demultiplex",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3088,13 +3088,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3111,7 +3111,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3169,6 +3169,11 @@ workflow run_wf {
       | map {id, state ->
         def newState = [:]
         println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
+        // No auto-detection of run information file (it is user provided),
+        // in this case the demultiplexer should also be specified.
+        assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
+          "you must also provide a demultiplexer"
+
         if (!state.run_information) {
           println("Run information was not specified, auto-detecting...")
           // The supported_platforms hashmap must be a 1-on-1 mapping
@@ -3206,7 +3211,7 @@ workflow run_wf {
             "found in input directory."
 
           // When autodetecting, the demultiplexer must be set if the run information was found
-          assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
+          assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
             "Please report this as a bug."
 
           // When autodetecting, the found demultiplexer must match
@@ -3226,7 +3231,7 @@ workflow run_wf {
             "run_information": run_information,
             "demultiplexer": demultiplexer,
           ]
-        }
+        } // end auto-detection logic
 
         if (newState.demultiplexer in ["bclconvert"]) {
           // Do not add InterOp to state because we generate the summary csv's in the next

target/nextflow/demultiplex/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'Demultiplexing of raw sequencing data'
 }
 

target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -141,12 +141,12 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -160,7 +160,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.3.0
+// interop_summary_to_csv v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "interop_summary_to_csv",
   "namespace" : "io",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2947,7 +2947,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2977,13 +2977,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3000,7 +3000,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3423,7 +3423,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/interop_summary_to_csv/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/interop_summary_to_csv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
 }
 
 process.container = 'nextflow/bash:latest'

target/nextflow/io/publish/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -170,12 +170,12 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -189,7 +189,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish/main.nf

@@ -1,4 +1,4 @@
-// publish v0.3.0
+// publish v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish",
   "namespace" : "io",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2989,7 +2989,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3012,13 +3012,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3035,7 +3035,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3481,7 +3481,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'Publish the processed results of the run'
 }
 

target/nextflow/io/untar/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -148,12 +148,12 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -167,7 +167,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/untar/main.nf

@@ -1,4 +1,4 @@
-// untar v0.3.0
+// untar v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "untar",
   "namespace" : "io",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2966,7 +2966,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2989,13 +2989,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3012,7 +3012,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3465,7 +3465,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/untar/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }
 

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

@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.3.0"
+version: "v0.3.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -13,6 +13,32 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--run_information"
+    description: "CSV file containing sample information, which will be used as \n\
+      input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\n\
+      or 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect\
+      \ the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--demultiplexer"
+    description: "Demultiplexer to use, choice depends on the provider\nof the instrument\
+      \ that was used to generate the data.\nWhen not using --sample_sheet, specifying\
+      \ this argument is not\nrequired.\n"
+    info: null
+    required: false
+    choices:
+    - "bases2fastq"
+    - "bclconvert"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Annotation flags"
   arguments:
   - type: "boolean_true"
@@ -156,15 +182,15 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "c9cf5854796b31767c70848bcaf9aa42648d0bd7"
-  git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-9-gc9cf585"
+  git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9"
+  git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.0-4-g35e1ab8"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
 package_config:
   name: "demultiplex"
-  version: "v0.3.0"
+  version: "v0.3.1"
   description: "Demultiplexing pipeline\n"
   info:
     test_resources:
@@ -178,7 +204,7 @@ package_config:
     \ := '$id'\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/runner/main.nf

@@ -1,4 +1,4 @@
-// runner v0.3.0
+// runner v0.3.1
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "runner",
-  "version" : "v0.3.0",
+  "version" : "v0.3.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2820,6 +2820,30 @@ meta = [
           "direction" : "input",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--run_information",
+          "description" : "CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\nor 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--demultiplexer",
+          "description" : "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
+          "required" : false,
+          "choices" : [
+            "bases2fastq",
+            "bclconvert"
+          ],
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     },
@@ -3003,13 +3027,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "c9cf5854796b31767c70848bcaf9aa42648d0bd7",
-    "git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-9-gc9cf585"
+    "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9",
+    "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.0-4-g35e1ab8"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.3.0",
+    "version" : "v0.3.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3026,7 +3050,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3065,9 +3089,11 @@ workflow run_wf {
       | demultiplex.run(
         fromState: [
           "input": "input",
+          "run_information": "run_information",
+          "demultiplexer": "demultiplexer",
           "output": "fastq",
           "output_falco": "qc/fastqc",
-          "output_multiqc": "qc/multiqc_report.html",
+          "output_multiqc": "qc/multiqc_report.html"
         ],
         toState: { id, result, state ->
           state + result

target/nextflow/runner/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.1'
   description = 'Runner for demultiplexing of raw sequencing data'
 }
 

target/nextflow/runner/nextflow_schema.json

@@ -23,6 +23,28 @@
             }
     
 
+        ,
+                "run_information": {
+                "type":
+                "string",
+                "description": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer",
+                "help_text": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called \u0027SampleSheet.csv\u0027 (Illumina)\nor \u0027RunManifest.csv\u0027 (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
+            
+            }
+    
+
+        ,
+                "demultiplexer": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data",
+                "help_text": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
+                "enum": ["bases2fastq", "bclconvert"]
+            
+            
+            }
+    
+
 }
 },