Build branch main with version main (dd1f934)

Build pipeline: viash-hub.demultiplex.main-v6krs Source commit: dd1f93487f Source message: Add check for the presence of a 'CopyComplete.txt' file (#34)
2025-01-14 12:10:26 +00:00
parent 8c1737e627
commit eb8d600efc
27 changed files with 177 additions and 58 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,10 @@
+# demultiplex v0.3.5
+
+## Minor updates
+
+* In case Illumina data is detected in the input folder, check for the presence of the 'copyComplete.txt' file.
+  This check can be disabled using `--skip_copycomplete_check` (PR #34).
+
 # demultiplex v0.3.4

 ## Minor updates
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -53,6 +53,14 @@ argument_groups:
        direction: "output"
        required: true
        default: "$id/run_information.csv"
+  - name: "Other arguments"
+    arguments:
+      - name: --skip_copycomplete_check
+        type: boolean_true
+        description: |
+          Disable the check for the presence of a "CopyComplete.txt" file in input
+          directory in case of Illumina data.
+        
 resources:
  - type: nextflow_script
    path: main.nf
--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -94,6 +94,10 @@ workflow run_wf {
          // step based on the run dir, not the InterOp dir.
          def interop_dir = state.input.resolve("InterOp")
          assert interop_dir.isDirectory(): "Expected InterOp directory to be present."
+
+          def copycomplete_file = state.input.resolve("CopyComplete.txt")
+          assert (copycomplete_file.isFile() || state.skip_copycomplete_check): 
+            "'CopyComplete.txt' file was not found!"
        }

        def resultState = state + newState
--- a/src/runner/config.vsh.yaml
+++ b/src/runner/config.vsh.yaml
@@ -49,7 +49,13 @@ argument_groups:
        type: file
        direction: output
        default: "qc/multiqc_report.html"
-
+  - name: "Other arguments"
+    arguments:
+      - name: --skip_copycomplete_check
+        type: boolean_true
+        description: |
+          Disable the check for the presence of a "CopyComplete.txt" file in input
+          directory in case of Illumina data.
 resources:
  - type: nextflow_script
    path: main.nf
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -24,6 +24,7 @@ workflow run_wf {
            "input": state.input,
            "run_information": state.run_information,
            "demultiplexer": state.demultiplexer,
+            "skip_copycomplete_check": state.skip_copycomplete_check,
            "output": "fastq",
            "output_falco": "qc/fastqc",
            "output_multiqc": "qc/multiqc_report.html",
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -149,9 +149,9 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -454,9 +454,9 @@ 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="2025-01-14T11:34:29Z"
+LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983"
+LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -199,9 +199,9 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -450,9 +450,9 @@ 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="2025-01-14T11:34:29Z"
+LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983"
+LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -450,9 +450,9 @@ 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="2025-01-14T11:34:29Z"
+LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983"
+LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -147,9 +147,9 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3216,9 +3216,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -141,9 +141,9 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -3209,9 +3209,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -96,6 +96,14 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+- name: "Other arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--skip_copycomplete_check"
+    description: "Disable the check for the presence of a \"CopyComplete.txt\" file\
+      \ in input\ndirectory in case of Illumina data.\n"
+    info: null
+    direction: "input"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -239,9 +247,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3147,6 +3147,17 @@ meta = [
          "multiple_sep" : ";"
        }
      ]
+    },
+    {
+      "name" : "Other arguments",
+      "arguments" : [
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_copycomplete_check",
+          "description" : "Disable the check for the presence of a \\"CopyComplete.txt\\" file in input\ndirectory in case of Illumina data.\n",
+          "direction" : "input"
+        }
+      ]
    }
  ],
  "resources" : [
@@ -3345,9 +3356,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3495,6 +3506,10 @@ workflow run_wf {
          // step based on the run dir, not the InterOp dir.
          def interop_dir = state.input.resolve("InterOp")
          assert interop_dir.isDirectory(): "Expected InterOp directory to be present."
+
+          def copycomplete_file = state.input.resolve("CopyComplete.txt")
+          assert (copycomplete_file.isFile() || state.skip_copycomplete_check): 
+            "'CopyComplete.txt' file was not found!"
        }

        def resultState = state + newState
--- a/target/nextflow/demultiplex/nextflow_schema.json
+++ b/target/nextflow/demultiplex/nextflow_schema.json
@@ -109,6 +109,27 @@
            }
    

+}
+},
+    
+    
+    "other arguments" : {
+    "title": "Other arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "skip_copycomplete_check": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n"
+            ,
+                "default":false
+            }
+    
+
 }
 },
    
@@ -153,6 +174,10 @@
    "$ref": "#/definitions/output arguments"
    },

+    {
+    "$ref": "#/definitions/other arguments"
+    },
+
    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -149,9 +149,9 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -3221,9 +3221,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -199,9 +199,9 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3280,9 +3280,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
 package_config:
  name: "demultiplex"
  version: "main"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -3233,9 +3233,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -84,6 +84,14 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+- name: "Other arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--skip_copycomplete_check"
+    description: "Disable the check for the presence of a \"CopyComplete.txt\" file\
+      \ in input\ndirectory in case of Illumina data.\n"
+    info: null
+    direction: "input"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -187,9 +195,9 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.1"
-  git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983"
-  git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-15-g8da2bf2"
+  git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
+  git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-16-gdd1f934"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3133,6 +3133,17 @@ meta = [
          "multiple_sep" : ";"
        }
      ]
+    },
+    {
+      "name" : "Other arguments",
+      "arguments" : [
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_copycomplete_check",
+          "description" : "Disable the check for the presence of a \\"CopyComplete.txt\\" file in input\ndirectory in case of Illumina data.\n",
+          "direction" : "input"
+        }
+      ]
    }
  ],
  "resources" : [
@@ -3265,9 +3276,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.1",
-    "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983",
-    "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-15-g8da2bf2"
+    "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9",
+    "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-16-gdd1f934"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3339,6 +3350,7 @@ workflow run_wf {
            "input": state.input,
            "run_information": state.run_information,
            "demultiplexer": state.demultiplexer,
+            "skip_copycomplete_check": state.skip_copycomplete_check,
            "output": "fastq",
            "output_falco": "qc/fastqc",
            "output_multiqc": "qc/multiqc_report.html",
--- a/target/nextflow/runner/nextflow_schema.json
+++ b/target/nextflow/runner/nextflow_schema.json
@@ -109,6 +109,27 @@
            }
    

+}
+},
+    
+    
+    "other arguments" : {
+    "title": "Other arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "skip_copycomplete_check": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n"
+            ,
+                "default":false
+            }
+    
+
 }
 },
    
@@ -157,6 +178,10 @@
    "$ref": "#/definitions/output arguments"
    },

+    {
+    "$ref": "#/definitions/other arguments"
+    },
+
    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }