Build branch main with version main (0e87de8)

Build pipeline: viash-hub.htrnaseq.main-29nvl

Source commit: 0e87de80bc

Source message: Bump craftbox to v0.2.0 (#62)

target/nextflow/stats/combine_star_logs/.config.vsh.yaml

@@ -83,6 +83,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -201,9 +204,9 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -234,7 +237,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: '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 := 'main'"

target/nextflow/stats/combine_star_logs/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/combine_star_logs/main.nf

@@ -3139,6 +3139,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3290,9 +3295,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3311,7 +3316,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'main'"

target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml

@@ -69,6 +69,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 test_resources:
 - type: "python_script"
   path: "test.py"
@@ -185,9 +188,9 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -218,7 +221,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: '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 := 'main'"

target/nextflow/stats/generate_pool_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/generate_pool_statistics/main.nf

@@ -3127,6 +3127,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "test_resources" : [
@@ -3274,9 +3279,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3295,7 +3300,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'main'"

target/nextflow/stats/generate_well_statistics/.config.vsh.yaml

@@ -135,6 +135,9 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "Generate summary statistics from BAM files generated by STAR solo."
 test_resources:
 - type: "python_script"
@@ -267,9 +270,9 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
   name: "htrnaseq"
   version: "main"
@@ -300,7 +303,8 @@ package_config:
   config_mods:
   - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
     \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: '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 := 'main'"

target/nextflow/stats/generate_well_statistics/_viash.yaml

@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh

target/nextflow/stats/generate_well_statistics/main.nf

@@ -3199,6 +3199,11 @@ meta = [
       "type" : "file",
       "path" : "/src/config/labels.config",
       "dest" : "nextflow_labels.config"
+    },
+    {
+      "type" : "file",
+      "path" : "/_viash.yaml",
+      "dest" : "_viash.yaml"
     }
   ],
   "description" : "Generate summary statistics from BAM files generated by STAR solo.",
@@ -3369,9 +3374,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957",
+    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-6-ga3b7ae3"
+    "git_tag" : "v0.7.2-9-g0e87de8"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3390,7 +3395,7 @@ meta = [
     "source" : "src",
     "target" : "target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: '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 := 'main'"