Build branch main with version main (1e1ffb3)

Build pipeline: vsh-ci-dev-jsbwk

Source commit: 1e1ffb315f

Source message: Merge pull request #17 from viash-hub/add_biobox_modules

- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub

target/executable/picard_markduplicates/.config.vsh.yaml

@@ -0,0 +1,218 @@
+name: "picard_markduplicates"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bam"
+    description: "Input BAM file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fasta"
+    description: "Reference genome FASTA file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fai"
+    description: "Reference genome FASTA index"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_picard_args"
+    description: "Additional argument to be passed to Picard MarkDuplicates"
+    info: null
+    default:
+    - "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT\
+      \ --TMP_DIR tmp"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_bam"
+    description: "BAM file with duplicate reads marked/removed"
+    info: null
+    default:
+    - "$id.MarkDuplicates.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bai"
+    description: "An optional BAM index file. If desired, --CREATE_INDEX must be passed\
+      \ as a flag"
+    info: null
+    default:
+    - "$id.MarkDuplicates.bam.bai"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--metrics"
+    description: "Duplicate metrics file generated by picard"
+    info: null
+    default:
+    - "$id.MarkDuplicates.metrics.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Locate and tag duplicate reads in a BAM file\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "genome.fasta"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/picard/markduplicates/main.nf"
+    - "modules/nf-core/picard/markduplicates/meta.yml"
+    last_sha: "55398de6ab7577acfe9b1180016a93d7af7eb859"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y build-essential openjdk-17-jdk wget\
+      \ && \\\nwget --no-check-certificate https://github.com/broadinstitute/picard/releases/download/3.1.1/picard.jar\
+      \ && \\\nmv picard.jar /usr/local/bin \n"
+    env:
+    - "PICARD=/usr/local/bin/picard.jar"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/picard_markduplicates/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/picard_markduplicates"
+  executable: "target/executable/picard_markduplicates/picard_markduplicates"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+package_config:
+  version: "main"
+  info:
+    test_resources:
+    - path: "gs://viash-hub-test-data/rnaseq/v1"
+      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'"
+  organization: "vsh"