Build branch main with version main (da414e7)

Build pipeline: viash-hub.biobox.main-7dwhr

Source commit: da414e72c6

Source message: Add star solo component (#62)

* add star solo component

* change arguments from camelCase to snake_case

* get rid of multiple_sep

* drop star_solo component and just add arguments to star_align_reads

* Update src/star/star_align_reads/script.py

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>

---------

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>

target/executable/seqtk/seqtk_sample/.config.vsh.yaml

@@ -0,0 +1,199 @@
+name: "seqtk_sample"
+namespace: "seqtk"
+version: "main"
+authors:
+- name: "Jakub Majercik"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "jakub@data-intuitive.com"
+      github: "jakubmajercik"
+      linkedin: "jakubmajercik"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatics Engineer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "The input FASTA/Q file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The output FASTA/Q file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "integer"
+    name: "--seed"
+    description: "Seed for random generator."
+    info: null
+    example:
+    - 42
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--fraction_number"
+    description: "Fraction or number of sequences to sample."
+    info: null
+    example:
+    - 0.1
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--two_pass_mode"
+    description: "Twice as slow but with much reduced memory"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Subsamples sequences from FASTA/Q files."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "sample"
+- "FASTA"
+- "FASTQ"
+license: "MIT"
+links:
+  repository: "https://github.com/lh3/seqtk/tree/v1.4"
+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: "quay.io/biocontainers/seqtk:1.4--he4a0461_2"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/seqtk/seqtk_sample/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/seqtk/seqtk_sample"
+  executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
+  viash_version: "0.9.0-RC6"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"