Build branch v0.4 with version v0.4.1 (cc1c33e)

Build pipeline: viash-hub.demultiplex.v0.4-m2h96 Source commit: cc1c33e8fe Source message: Bump version to v0.4.1
2025-07-25 09:20:19 +00:00
parent 77b709a2bc
commit 997c850d5f
51 changed files with 4651 additions and 311 deletions
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.4.0"
+version: "v0.4.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -76,6 +76,9 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Combine fastq files from across samples into one event with a list of\
  \ fastq files per orientation."
 info: null
@@ -165,12 +168,12 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "d331781d1a699792462d6e2d5205ffc51ab3ecef"
+  git_commit: "cc1c33e8fe4252c512dce4629bb2fa173684d7b5"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-32-gd331781"
+  git_tag: "v0.1.1-37-gcc1c33e"
 package_config:
  name: "demultiplex"
-  version: "v0.4.0"
+  version: "v0.4.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -183,10 +186,10 @@ package_config:
  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
-    )'\n"
+    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/_viash.yaml
+++ b/target/nextflow/dataflow/combine_samples/_viash.yaml
@@ -0,0 +1,21 @@
+name: demultiplex
+version: v0.4.1
+description: |
+  Demultiplexing pipeline
+license: MIT
+keywords: [bioinformatics, sequence, demultiplexing, pipeline]
+links:
+  issue_tracker: https://github.com/viash-hub/demultiplex/issues
+  repository: https://github.com/viash-hub/demultiplex
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/demultiplex/v4
+      dest: testData
+viash_version: 0.9.4
+config_mods: |
+  .requirements.commands += ['ps']
+  .runners[.type == 'nextflow'].directives.tag := '$id'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+organization: vsh
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.4.0
+// combine_samples v0.4.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3125,6 +3125,11 @@ meta = [
      "type" : "file",
      "path" : "/src/config/labels.config",
      "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
    }
  ],
  "description" : "Combine fastq files from across samples into one event with a list of fastq files per orientation.",
@@ -3230,13 +3235,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "d331781d1a699792462d6e2d5205ffc51ab3ecef",
+    "git_commit" : "cc1c33e8fe4252c512dce4629bb2fa173684d7b5",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-32-gd331781"
+    "git_tag" : "v0.1.1-37-gcc1c33e"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3250,10 +3255,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/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 = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.4.0"
+version: "v0.4.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -52,6 +52,9 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "From a directory containing fastq files, gather the files per sample\
  \ \nand validate according to the contents of the sample sheet.\n"
 test_resources:
@@ -156,12 +159,12 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.4"
-  git_commit: "d331781d1a699792462d6e2d5205ffc51ab3ecef"
+  git_commit: "cc1c33e8fe4252c512dce4629bb2fa173684d7b5"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-32-gd331781"
+  git_tag: "v0.1.1-37-gcc1c33e"
 package_config:
  name: "demultiplex"
-  version: "v0.4.0"
+  version: "v0.4.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -174,10 +177,10 @@ package_config:
  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
-    )'\n"
+    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
@@ -0,0 +1,21 @@
+name: demultiplex
+version: v0.4.1
+description: |
+  Demultiplexing pipeline
+license: MIT
+keywords: [bioinformatics, sequence, demultiplexing, pipeline]
+links:
+  issue_tracker: https://github.com/viash-hub/demultiplex/issues
+  repository: https://github.com/viash-hub/demultiplex
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/demultiplex/v4
+      dest: testData
+viash_version: 0.9.4
+config_mods: |
+  .requirements.commands += ['ps']
+  .runners[.type == 'nextflow'].directives.tag := '$id'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+organization: vsh
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.4.0
+// gather_fastqs_and_validate v0.4.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.4.0",
+  "version" : "v0.4.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3098,6 +3098,11 @@ meta = [
      "type" : "file",
      "path" : "/src/config/labels.config",
      "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
    }
  ],
  "description" : "From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n",
@@ -3227,13 +3232,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "d331781d1a699792462d6e2d5205ffc51ab3ecef",
+    "git_commit" : "cc1c33e8fe4252c512dce4629bb2fa173684d7b5",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-32-gd331781"
+    "git_tag" : "v0.1.1-37-gcc1c33e"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.4.0",
+    "version" : "v0.4.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3247,10 +3252,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.4.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.4.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/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 = 'v0.4.0'
+  version = 'v0.4.1'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }