Build branch main with version main (64a371e)

Build pipeline: viash-hub.demultiplex.main-lcwkk Source commit: 64a371e168 Source message: Update CHANGELOG for 0.2.0 (#25)
2024-12-11 09:03:18 +00:00
parent fcc3a4d62e
commit 73c077fd82
36 changed files with 9615 additions and 84 deletions
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -141,9 +141,9 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.0"
-  git_commit: "6e6be28b85ab619214ae05a017a33498c0dc8890"
-  git_remote: "https://x-access-token:ghs_iopCikoFK5KlWGbHHLIwAf82AMtbiI0fzew1@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-5-g6e6be28"
+  git_commit: "64a371e168472c987d9ec61b0373b0e28762dfcd"
+  git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-7-g64a371e"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -156,7 +156,8 @@ package_config:
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".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 := '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
@@ -470,9 +470,9 @@ 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="2024-12-05T10:21:34Z"
+LABEL org.opencontainers.image.created="2024-12-11T08:48:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="6e6be28b85ab619214ae05a017a33498c0dc8890"
+LABEL org.opencontainers.image.revision="64a371e168472c987d9ec61b0373b0e28762dfcd"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -0,0 +1,202 @@
+name: "publish"
+namespace: "io"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Directory to write fastq data to"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_falco"
+    description: "Directory to write falco output to"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_multiqc"
+    description: "Directory to write falco output to"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_falco"
+    info: null
+    default:
+    - "qc/fastqc"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_multiqc"
+    info: null
+    default:
+    - "qc/multiqc_report.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "code.sh"
+  is_executable: true
+description: "Publish the processed results of the run"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/io/publish/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/io/publish"
+  executable: "target/executable/io/publish/publish"
+  viash_version: "0.9.0"
+  git_commit: "64a371e168472c987d9ec61b0373b0e28762dfcd"
+  git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-7-g64a371e"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "gs://viash-hub-test-data/demultiplex/v2/"
+      dest: "testData"
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".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 := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -148,9 +148,9 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "6e6be28b85ab619214ae05a017a33498c0dc8890"
-  git_remote: "https://x-access-token:ghs_iopCikoFK5KlWGbHHLIwAf82AMtbiI0fzew1@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-5-g6e6be28"
+  git_commit: "64a371e168472c987d9ec61b0373b0e28762dfcd"
+  git_remote: "https://x-access-token:ghs_NEnBDPGgmRYfKlNL6VeMqiNleTP4aC2s2yz6@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-7-g64a371e"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -163,7 +163,8 @@ package_config:
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".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 := 'main'"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -476,9 +476,9 @@ 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="2024-12-05T10:21:34Z"
+LABEL org.opencontainers.image.created="2024-12-11T08:48:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="6e6be28b85ab619214ae05a017a33498c0dc8890"
+LABEL org.opencontainers.image.revision="64a371e168472c987d9ec61b0373b0e28762dfcd"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER