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/bbmap_bbsplit/.config.vsh.yaml

@@ -0,0 +1,249 @@
+name: "bbmap_bbsplit"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "Sample ID"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files, either one or two (paired)"
+    info: null
+    example:
+    - "sample.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--primary_ref"
+    description: "Primary reference FASTA"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_fasta_list"
+    description: "Path to comma-separated file containing a list of reference genomes\
+      \ to filter reads against with BBSplit."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--only_build_index"
+    description: "true = only build index; false = mapping"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--built_bbsplit_index"
+    description: "Directory with index files"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fastq_1"
+    description: "Output file for read 1."
+    info: null
+    default:
+    - "$id.$key.read_1.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Output file for read 2."
+    info: null
+    default:
+    - "$id.$key.read_2.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_index"
+    description: "Directory with index files"
+    info: null
+    default:
+    - "BBSplit_index"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Split sequencing reads by mapping them to multiple references simultaneously.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genome.fasta"
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+- type: "file"
+  path: "sarscov2.fa"
+- type: "file"
+  path: "human.fa"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/bbmap/bbsplit/main.nf"
+    - "modules/nf-core/bbmap/bbsplit/meta.yml"
+    last_sha: "277bd337739a8b8f753fa7b5eda6743b9b6acb89"
+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\
+      \ tar && \\\nwget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz\
+      \ && \\\ntar xzf BBMap_39.01.tar.gz && \\\ncp -r bbmap/* /usr/local/bin\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bbmap_bbsplit/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bbmap_bbsplit"
+  executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
+  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"

target/executable/bedtools_genomecov/.config.vsh.yaml

@@ -0,0 +1,189 @@
+name: "bedtools_genomecov"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity."
+    info: null
+    required: false
+    choices:
+    - "unstranded"
+    - "forward"
+    - "reverse"
+    - "auto"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bam"
+    description: "Genome BAM file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_bedtools_args"
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--bedgraph_forward"
+    info: null
+    default:
+    - "$id.forward.bedgraph"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bedgraph_reverse"
+    info: null
+    default:
+    - "$id.reverse.bedgraph"
+    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: "Compute BEDGRAPH (-bg) summaries of feature coverage"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "chr19.bam"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/bedtools_genomecov.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+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 wget && \\\nwget --no-check-certificate\
+      \ https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static\
+      \ && \\\nmv bedtools.static /usr/local/bin/bedtools && \\\nchmod a+x /usr/local/bin/bedtools\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bedtools_genomecov/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools_genomecov"
+  executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
+  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"

target/executable/cat_additional_fasta/.config.vsh.yaml

@@ -0,0 +1,193 @@
+name: "cat_additional_fasta"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--fasta"
+    description: "Path to FASTA genome file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Path to GTF annotation file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--additional_fasta"
+    description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\
+      \ sequences."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--biotype"
+    description: "Biotype value to use when appending entries to GTF file when additional\
+      \ fasta file is provided."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fasta_output"
+    description: "Concatenated FASTA file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf_output"
+    description: "Concatenated GTF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+description: "Concatenate addional fasta file to reference FASTA and GTF files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genome.fasta"
+- type: "file"
+  path: "genes.gtf.gz"
+- type: "file"
+  path: "gfp.fa.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/cat_additional_fasta.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+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: "python"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/cat_additional_fasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/cat_additional_fasta"
+  executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
+  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"

target/executable/cat_fastq/.config.vsh.yaml

@@ -0,0 +1,180 @@
+name: "cat_fastq"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--read_1"
+    description: "Read 1 fastq files to be concatenated"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--read_2"
+    description: "Read 2 fastq files to be concatenated"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fastq_1"
+    description: "Concatenated read 1 fastq"
+    info: null
+    default:
+    - "$id.read_1.merged.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Concatenated read 2 fastq"
+    info: null
+    default:
+    - "$id.read_2.merged.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Concatenate multiple fastq files"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357071_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+- type: "file"
+  path: "SRR6357071_2.fastq.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/cat/fastq/main.nf"
+    - "modules/nf-core/cat/fastq/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/cat_fastq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/cat_fastq"
+  executable: "target/executable/cat_fastq/cat_fastq"
+  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"

target/executable/deseq2_qc/.config.vsh.yaml

@@ -0,0 +1,248 @@
+name: "deseq2_qc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--counts"
+    description: "Count file matrix where rows are genes and columns are samples"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--pca_header_multiqc"
+    info: null
+    default:
+    - "assets/multiqc/deseq2_pca_header.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--clustering_header_multiqc"
+    info: null
+    default:
+    - "assets/multiqc/deseq2_clustering_header.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--deseq2_vst"
+    description: "Use vst transformation instead of rlog with DESeq2"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_args"
+    info: null
+    default:
+    - "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_args2"
+    info: null
+    default:
+    - "star_salmon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--deseq2_output"
+    info: null
+    default:
+    - "deseq2"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--pca_multiqc"
+    info: null
+    default:
+    - "deseq2.pca.vals_mqc.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--dists_multiqc"
+    info: null
+    default:
+    - "deseq2.sample.dists_mqc.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "deseq2_qc.r"
+description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\
+  \ in the counts files\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "counts.tsv"
+- type: "file"
+  path: "deseq2_pca_header.txt"
+- type: "file"
+  path: "deseq2_clustering_header.txt"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/deseq2_qc.nf"
+    last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
+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: "apt"
+    packages:
+    - "r-base"
+    - "libcurl4-openssl-dev"
+    - "libssl-dev"
+    - "libxml2-dev"
+    interactive: false
+  - type: "r"
+    cran:
+    - "optparse"
+    - "ggplot2"
+    - "RColorBrewer"
+    - "pheatmap"
+    bioc:
+    - "DESeq2"
+    url:
+    - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
+    bioc_force_install: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/deseq2_qc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/deseq2_qc"
+  executable: "target/executable/deseq2_qc/deseq2_qc"
+  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"

target/executable/deseq2_qc/deseq2_qc.r

@@ -0,0 +1,246 @@
+#!/usr/bin/env Rscript
+
+################################################
+################################################
+## REQUIREMENTS                               ##
+################################################
+################################################
+
+## PCA, HEATMAP AND SCATTERPLOTS FOR SAMPLES IN COUNTS FILE
+## - SAMPLE NAMES HAVE TO END IN e.g. "_R1" REPRESENTING REPLICATE ID. LAST 3 CHARACTERS OF SAMPLE NAME WILL BE TRIMMED TO OBTAIN GROUP ID FOR DESEQ2 COMPARISONS.
+## - PACKAGES BELOW NEED TO BE AVAILABLE TO LOAD WHEN RUNNING R
+
+################################################
+################################################
+## LOAD LIBRARIES                             ##
+################################################
+################################################
+
+library(optparse)
+library(DESeq2)
+library(ggplot2)
+library(RColorBrewer)
+library(pheatmap)
+
+################################################
+################################################
+## PARSE COMMAND-LINE PARAMETERS              ##
+################################################
+################################################
+
+option_list <- list(
+    make_option(c("-i", "--count_file"), type="character", default=NULL, metavar="path", help="Count file matrix where rows are genes and columns are samples."),
+    make_option(c("-f", "--count_col"), type="integer", default=3, metavar="integer", help="First column containing sample count data."),
+    make_option(c("-d", "--id_col"), type="integer", default=1, metavar="integer", help="Column containing identifiers to be used."),
+    make_option(c("-r", "--sample_suffix"), type="character", default='', metavar="string", help="Suffix to remove after sample name in columns e.g. '.rmDup.bam' if 'DRUG_R1.rmDup.bam'."),
+    make_option(c("-p", "--outprefix"), type="character", default='deseq2', metavar="string" , help="Output prefix."),
+    make_option(c("-v", "--vst"), type="logical", default=FALSE, metavar="boolean", help="Run vst transform instead of rlog."),
+    make_option(c("-c", "--cores"), type="integer", default=1, metavar="integer", help="Number of cores."), 
+    make_option(c("-o", "--outdir"), type="character", default="./", metavar="path", help="Output directory.")
+)
+
+opt_parser <- OptionParser(option_list=option_list)
+opt        <- parse_args(opt_parser)
+if (is.null(opt$count_file)){
+    print_help(opt_parser)
+    stop("Please provide a counts file.", call.=FALSE)
+}
+
+################################################
+################################################
+## READ IN COUNTS FILE                        ##
+################################################
+################################################
+
+count.table           <- read.delim(file=opt$count_file,header=TRUE, row.names=NULL)
+rownames(count.table) <- count.table[,opt$id_col]
+count.table           <- count.table[,opt$count_col:ncol(count.table),drop=FALSE]
+colnames(count.table) <- gsub(opt$sample_suffix,"",colnames(count.table))
+colnames(count.table) <- gsub(pattern='\\.$', replacement='', colnames(count.table))
+
+################################################
+################################################
+## RUN DESEQ2                                 ##
+################################################
+################################################
+
+if (file.exists(opt$outdir) == FALSE) {
+    dir.create(opt$outdir, recursive=TRUE)
+}
+setwd(opt$outdir)
+
+samples.vec     <- colnames(count.table)
+name_components <- strsplit(samples.vec, "_")
+n_components    <- length(name_components[[1]])
+decompose       <- n_components!=1 && all(sapply(name_components, length)==n_components)
+coldata         <- data.frame(samples.vec, sample=samples.vec, row.names=1)
+if (decompose) {
+    groupings        <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
+    n_distinct       <- sapply(groupings, function(grp) length(unique(grp)))
+    groupings        <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
+    if (ncol(groupings)!=0) {
+        names(groupings) <- paste0("Group", 1:ncol(groupings))
+        coldata <- cbind(coldata, groupings)
+    } else {
+        decompose <- FALSE
+    }
+}
+
+DDSFile <- paste(opt$outprefix,".dds.RData",sep="")
+
+counts  <- count.table[,samples.vec,drop=FALSE]
+dds     <- DESeqDataSetFromMatrix(countData=round(counts), colData=coldata, design=~ 1)
+dds     <- estimateSizeFactors(dds)
+if (min(dim(count.table))<=1)  { # No point if only one sample, or one gene
+    save(dds,file=DDSFile)
+    saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
+    warning("Not enough samples or genes in counts file for PCA.", call.=FALSE)
+    quit(save = "no", status = 0, runLast = FALSE)
+}
+if (!opt$vst) {
+    vst_name <- "rlog"
+    rld      <- rlog(dds)
+} else {
+    vst_name <- "vst"
+    rld      <- varianceStabilizingTransformation(dds)
+}
+
+assay(dds, vst_name) <- assay(rld)
+save(dds,file=DDSFile)
+saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
+
+################################################
+################################################
+## PLOT QC                                    ##
+################################################
+################################################
+
+##' PCA pre-processeor
+##'
+##' Generate all the necessary information to plot PCA from a DESeq2 object
+##' in which an assay containing a variance-stabilised matrix of counts is
+##' stored. Copied from DESeq2::plotPCA, but with additional ability to
+##' say which assay to run the PCA on.
+##'
+##' @param object The DESeq2DataSet object.
+##' @param ntop number of top genes to use for principla components, selected by highest row variance.
+##' @param assay the name or index of the assay that stores the variance-stabilised data.
+##' @return A data.frame containing the projected data alongside the grouping columns.
+##' A 'percentVar' attribute is set which includes the percentage of variation each PC explains,
+##' and additionally how much the variation within that PC is explained by the grouping variable.
+##' @author Gavin Kelly
+plotPCA_vst <- function (object,  ntop = 500, assay=length(assays(object))) {
+    rv         <- rowVars(assay(object, assay))
+    select     <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
+    pca        <- prcomp(t(assay(object, assay)[select, ]), center=TRUE, scale=FALSE)
+    percentVar <- pca$sdev^2/sum(pca$sdev^2)
+    df         <- cbind( as.data.frame(colData(object)), pca$x)
+    #Order points so extreme samples are more likely to get label
+    ord        <- order(abs(rank(df$PC1)-median(df$PC1)), abs(rank(df$PC2)-median(df$PC2)))
+    df         <- df[ord,]
+    attr(df, "percentVar") <- data.frame(PC=seq(along=percentVar), percentVar=100*percentVar)
+    return(df)
+}
+
+PlotFile <- paste(opt$outprefix,".plots.pdf",sep="")
+
+pdf(file=PlotFile, onefile=TRUE, width=7, height=7)
+## PCA
+ntop <- c(500, Inf)
+for (n_top_var in ntop) {
+    pca.data      <- plotPCA_vst(dds, assay=vst_name, ntop=n_top_var)
+    percentVar    <- round(attr(pca.data, "percentVar")$percentVar)
+    plot_subtitle <- ifelse(n_top_var==Inf, "All genes", paste("Top", n_top_var, "genes"))
+    pl <- ggplot(pca.data, aes(PC1, PC2, label=paste0(" ", sample, " "))) +
+        geom_point() +
+        geom_text(check_overlap=TRUE, vjust=0.5, hjust="inward") +
+        xlab(paste0("PC1: ",percentVar[1],"% variance")) +
+        ylab(paste0("PC2: ",percentVar[2],"% variance")) +
+        labs(title = paste0("First PCs on ", vst_name, "-transformed data"), subtitle = plot_subtitle) +
+        theme(legend.position="top",
+            panel.grid.major = element_blank(),
+            panel.grid.minor = element_blank(),
+            panel.background = element_blank(),
+            panel.border = element_rect(colour = "black", fill=NA, size=1))
+    print(pl)
+
+    if (decompose) {
+        pc_names <- paste0("PC", attr(pca.data, "percentVar")$PC)
+        long_pc <- reshape(pca.data, varying=pc_names, direction="long", sep="", timevar="component", idvar="pcrow")
+        long_pc <- subset(long_pc, component<=5)
+        long_pc_grp <- reshape(long_pc, varying=names(groupings), direction="long", sep="", timevar="grouper")
+        long_pc_grp <- subset(long_pc_grp, grouper<=5)
+        long_pc_grp$component <- paste("PC", long_pc_grp$component)
+        long_pc_grp$grouper <- paste0(long_pc_grp$grouper, c("st","nd","rd","th","th")[long_pc_grp$grouper], " prefix")
+        pl <- ggplot(long_pc_grp, aes(x=Group, y=PC)) +
+            geom_point() +
+            stat_summary(fun=mean, geom="line", aes(group = 1)) +
+            labs(x=NULL, y=NULL, subtitle = plot_subtitle, title="PCs split by sample-name prefixes") +
+            facet_grid(component~grouper, scales="free_x") +
+            scale_x_discrete(guide = guide_axis(n.dodge = 3))
+        print(pl)
+    }
+} # at end of loop, we'll be using the user-defined ntop if any, else all genes
+
+## WRITE PC1 vs PC2 VALUES TO FILE
+pca.vals           <- pca.data[,c("PC1","PC2")]
+colnames(pca.vals) <- paste0(colnames(pca.vals), ": ", percentVar[1:2], '% variance')
+pca.vals           <- cbind(sample = rownames(pca.vals), pca.vals)
+write.table(pca.vals, file = paste(opt$outprefix, ".pca.vals.txt", sep=""),
+            row.names = FALSE, col.names = TRUE, sep = "\t", quote = TRUE)
+
+## SAMPLE CORRELATION HEATMAP
+sampleDists      <- dist(t(assay(dds, vst_name)))
+sampleDistMatrix <- as.matrix(sampleDists)
+colors           <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
+pheatmap(
+    sampleDistMatrix,
+    clustering_distance_rows=sampleDists,
+    clustering_distance_cols=sampleDists,
+    col=colors,
+    main=paste("Euclidean distance between", vst_name, "of samples")
+)
+
+## WRITE SAMPLE DISTANCES TO FILE
+write.table(cbind(sample = rownames(sampleDistMatrix), sampleDistMatrix),file=paste(opt$outprefix, ".sample.dists.txt", sep=""),
+            row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE)
+dev.off()
+
+################################################
+################################################
+## SAVE SIZE FACTORS                          ##
+################################################
+################################################
+
+SizeFactorsDir <- "size_factors/"
+if (file.exists(SizeFactorsDir) == FALSE) {
+    dir.create(SizeFactorsDir, recursive=TRUE)
+}
+
+NormFactorsFile <- paste(SizeFactorsDir,opt$outprefix, ".size_factors.RData", sep="")
+
+normFactors <- sizeFactors(dds)
+save(normFactors, file=NormFactorsFile)
+
+for (name in names(sizeFactors(dds))) {
+    sizeFactorFile <- paste(SizeFactorsDir,name, ".txt", sep="")
+    write(as.numeric(sizeFactors(dds)[name]), file=sizeFactorFile)
+}
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+RLogFile <- "R_sessionInfo.log"
+
+sink(RLogFile)
+a <- sessionInfo()
+print(a)
+sink()
+
+################################################
+################################################
+################################################
+################################################

target/executable/dupradar/.config.vsh.yaml

@@ -0,0 +1,277 @@
+name: "dupradar"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "Sample ID"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "path to input alignment file in BAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf_annotation"
+    description: "path to GTF annotation file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--paired"
+    description: "add flag if input alignment file consists of paired reads"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "strandedness of input bam file reads (forward, reverse or unstranded\
+      \ (default, applicable to paired reads))"
+    info: null
+    required: false
+    choices:
+    - "forward"
+    - "reverse"
+    - "unstranded"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_dupmatrix"
+    description: "path to output file (txt) of duplicate tag counts"
+    info: null
+    default:
+    - "$id.dup_matrix.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_dup_intercept_mqc"
+    description: "path to output file (txt) of multiqc intercept value DupRadar"
+    info: null
+    default:
+    - "$id.dup_intercept_mqc.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duprate_exp_boxplot"
+    description: "path to output file (pdf) of distribution of expression box plot"
+    info: null
+    default:
+    - "$id.duprate_exp_boxplot.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duprate_exp_densplot"
+    description: "path to output file (pdf) of 2D density scatter plot of duplicate\
+      \ tag counts"
+    info: null
+    default:
+    - "$id.duprate_exp_densityplot.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duprate_exp_denscurve_mqc"
+    description: "path to output file (pdf) of density curve of gene duplication multiqc"
+    info: null
+    default:
+    - "$id.duprate_exp_density_curve_mqc.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_expression_histogram"
+    description: "path to output file (pdf) of distribution of RPK values per gene\
+      \ histogram"
+    info: null
+    default:
+    - "$id.expression_hist.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_intercept_slope"
+    description: "output file (txt) with progression of duplication rate value"
+    info: null
+    default:
+    - "$id.intercept_slope.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "dupradar.r"
+description: "Assessment of duplication rates in RNA-Seq datasets\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam"
+- type: "file"
+  path: "genes.gtf"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/dupradar.nf"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "r-base"
+    interactive: false
+  - type: "r"
+    bioc:
+    - "dupRadar"
+    bioc_force_install: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/dupradar/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/dupradar"
+  executable: "target/executable/dupradar/dupradar"
+  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"

target/executable/dupradar/dupradar.r

@@ -0,0 +1,154 @@
+#!/usr/bin/env Rscript
+
+# Command line argument processing
+args = commandArgs(trailingOnly=TRUE)
+if (length(args) < 5) {
+    stop("Usage: dupRadar.r <input.bam> <sample_id> <annotation.gtf> <strandDirection:0=unstranded/1=forward/2=reverse> <paired/single> <nbThreads> <R-package-location (optional)>", call.=FALSE)
+}
+
+message("paired_end is", args[5])
+message("the type is is", class(args[5]))
+
+input_bam <- args[1]
+output_prefix <- args[2]
+annotation_gtf <- args[3]
+stranded <- as.numeric(args[4])
+paired_end <- ifelse(args[5] == "true", TRUE, FALSE)
+threads <- as.numeric(args[6])
+
+bamRegex <- "(.+)\\.bam$"
+
+if(!(grepl(bamRegex, input_bam) && file.exists(input_bam) &&  (!file.info(input_bam)$isdir))) stop("First argument '<input.bam>' must be an existing file (not a directory) with '.bam' extension...")
+if(!(file.exists(annotation_gtf) &&  (!file.info(annotation_gtf)$isdir))) stop("Third argument '<annotation.gtf>' must be an existing file (and not a directory)...")
+if(is.na(stranded) || (!(stranded %in% (0:2)))) stop("Fourth argument <strandDirection> must be a numeric value in 0(unstranded)/1(forward)/2(reverse)...")
+if(is.na(threads) || (threads<=0)) stop("Fifth argument <nbThreads> must be a strictly positive numeric value...")
+
+# Debug messages (stderr)
+message("Input bam      (Arg 1): ", input_bam)
+message("Output basename(Arg 2): ", output_prefix)
+message("Input gtf      (Arg 3): ", annotation_gtf)
+message("Strandness     (Arg 4): ", c("unstranded", "forward", "reverse")[stranded+1])
+message("paired_end     (Arg 5): ", paired_end)
+message("Nb threads     (Arg 6): ", threads)
+message("R package loc. (Arg 7): ", ifelse(length(args) > 4, args[5], "Not specified"))
+
+
+# Load / install packages
+if (length(args) > 5) { .libPaths( c( args[6], .libPaths() ) ) }
+if (!require("dupRadar")){
+    source("http://bioconductor.org/biocLite.R")
+    biocLite("dupRadar", suppressUpdates=TRUE)
+    library("dupRadar")
+}
+if (!require("parallel")) {
+    install.packages("parallel", dependencies=TRUE, repos='http://cloud.r-project.org/')
+    library("parallel")
+}
+
+# Duplicate stats
+dm <- analyzeDuprates(input_bam, annotation_gtf, stranded, paired_end, threads)
+write.table(dm, file=paste(output_prefix, "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")
+
+# 2D density scatter plot
+pdf(paste0(output_prefix, "_duprateExpDens.pdf"))
+duprateExpDensPlot(DupMat=dm)
+title("Density scatter plot")
+mtext(output_prefix, side=3)
+dev.off()
+fit <- duprateExpFit(DupMat=dm)
+cat(
+    paste("- dupRadar Int (duprate at low read counts):", fit$intercept),
+    paste("- dupRadar Sl (progression of the duplication rate):", fit$slope),
+    fill=TRUE, labels=output_prefix,
+    file=paste0(output_prefix, "_intercept_slope.txt"), append=FALSE
+)
+
+# Create a multiqc file dupInt
+sample_name <- gsub("Aligned.sortedByCoord.out.markDups", "", output_prefix)
+line="#id: DupInt
+#plot_type: 'generalstats'
+#pconfig:
+#    dupRadar_intercept:
+#        title: 'dupInt'
+#        namespace: 'DupRadar'
+#        description: 'Intercept value from DupRadar'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+#        format: '{:.2f}%'
+Sample dupRadar_intercept"
+
+write(line,file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
+write(paste(sample_name, fit$intercept),file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
+
+# Get numbers from dupRadar GLM
+curve_x <- sort(log10(dm$RPK))
+curve_y = 100*predict(fit$glm, data.frame(x=curve_x), type="response")
+# Remove all of the infinite values
+infs = which(curve_x %in% c(-Inf,Inf))
+curve_x = curve_x[-infs]
+curve_y = curve_y[-infs]
+# Reduce number of data points
+curve_x <- curve_x[seq(1, length(curve_x), 10)]
+curve_y <- curve_y[seq(1, length(curve_y), 10)]
+# Convert x values back to real counts
+curve_x = 10^curve_x
+# Write to file
+line="#id: dupradar
+#section_name: 'DupRadar'
+#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
+#description: \"provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.
+#    This plot shows the general linear models - a summary of the gene duplication distributions. \"
+#pconfig:
+#    title: 'DupRadar General Linear Model'
+#    xLog: True
+#    xlab: 'expression (reads/kbp)'
+#    ylab: '% duplicate reads'
+#    ymax: 100
+#    ymin: 0
+#    tt_label: '<b>{point.x:.1f} reads/kbp</b>: {point.y:,.2f}% duplicates'
+#    xPlotLines:
+#        - color: 'green'
+#          dashStyle: 'LongDash'
+#          label:
+#                style: {color: 'green'}
+#                text: '0.5 RPKM'
+#                verticalAlign: 'bottom'
+#                y: -65
+#          value: 0.5
+#          width: 1
+#        - color: 'red'
+#          dashStyle: 'LongDash'
+#          label:
+#                style: {color: 'red'}
+#                text: '1 read/bp'
+#                verticalAlign: 'bottom'
+#                y: -65
+#          value: 1000
+#          width: 1"
+
+write(line,file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),append=TRUE)
+write.table(
+    cbind(curve_x, curve_y),
+    file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),
+    quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE,
+)
+
+# Distribution of expression box plot
+pdf(paste0(output_prefix, "_duprateExpBoxplot.pdf"))
+duprateExpBoxplot(DupMat=dm)
+title("Percent Duplication by Expression")
+mtext(output_prefix, side=3)
+dev.off()
+
+# Distribution of RPK values per gene
+pdf(paste0(output_prefix, "_expressionHist.pdf"))
+expressionHist(DupMat=dm)
+title("Distribution of RPK values per gene")
+mtext(output_prefix, side=3)
+dev.off()
+
+# Print sessioninfo to standard out
+print(output_prefix)
+citation("dupRadar")
+sessionInfo()

target/executable/fastqc/.config.vsh.yaml

@@ -0,0 +1,209 @@
+name: "fastqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files, either one or two (paired)"
+    info: null
+    example:
+    - "sample.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fastqc_html_1"
+    description: "FastQC HTML report for read 1."
+    info: null
+    default:
+    - "$id.read_1.fastqc.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_html_2"
+    description: "FastQC HTML report for read 2."
+    info: null
+    default:
+    - "$id.read_2.fastqc.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_zip_1"
+    description: "FastQC report archive for read 1."
+    info: null
+    default:
+    - "$id.read_1.fastqc.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_zip_2"
+    description: "FastQC report archive for read 2."
+    info: null
+    default:
+    - "$id.read_2.fastqc.zip"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.\
+  \ This component can take one or more files (by means of shell globbing) or a complete\
+  \ directory.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/fastqc/main.nf"
+    - "modules/nf-core/fastqc/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "fastqc"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fastqc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fastqc"
+  executable: "target/executable/fastqc/fastqc"
+  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"

target/executable/fq_subsample/.config.vsh.yaml

@@ -0,0 +1,188 @@
+name: "fq_subsample"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files to subsample"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_args"
+    description: "Extra arguments to pass to fq subsample"
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--output_1"
+    description: "Sampled read 1 fastq files"
+    info: null
+    default:
+    - "$id.read_1.subsampled.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_2"
+    description: "Sampled read 2 fastq files"
+    info: null
+    default:
+    - "$id.read_2.subsampled.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "fq subsample outputs a subset of records from single or paired FASTQ\
+  \ files. This requires a seed (--seed) to be set in ext.args\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/fq/subsample/main.nf"
+    - "modules/nf-core/fq/subsample/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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:
+    - "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
+      \ && \\\napt-get update && \\\napt-get install -y --no-install-recommends build-essential\
+      \ git-all curl && \\\ncurl https://sh.rustup.rs -sSf | sh -s -- -y && \\\n.\
+      \ \"$HOME/.cargo/env\" && \\\ngit clone --depth 1 --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git\
+      \ && \\\nmv fq /usr/local/ && cd /usr/local/fq && \\\ncargo install --locked\
+      \ --path . && \\\nmv /usr/local/fq/target/release/fq /usr/local/bin/\n"
+    env:
+    - "TZ=Europe/Brussels"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fq_subsample/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fq_subsample"
+  executable: "target/executable/fq_subsample/fq_subsample"
+  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"

target/executable/getchromsizes/.config.vsh.yaml

@@ -0,0 +1,178 @@
+name: "getchromsizes"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--fasta"
+    description: "Genome fasta files"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--sizes"
+    description: "File containing chromosome lengths"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fai"
+    description: "FASTA index file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gzi"
+    description: "Optional gzip index file for compressed inputs"
+    info: null
+    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: "Generates a FASTA file of chromosome sizes and a fasta index file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genome.fasta"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/custom/getchromsizes/main.nf"
+    - "modules/nf-core/custom/getchromsizes/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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 autoconf automake make gcc perl zlib1g-dev\
+      \ libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev curl\
+      \ bzip2 && \\\ncurl -fsSL https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2\
+      \ -o samtools-1.18.tar.bz2 && \\\ntar -xjf samtools-1.18.tar.bz2 && \\\nrm samtools-1.18.tar.bz2\
+      \ && \\\ncd samtools-1.18 && \\\n./configure && \\\nmake && \\\nmake install\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/getchromsizes/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/getchromsizes"
+  executable: "target/executable/getchromsizes/getchromsizes"
+  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"

target/executable/gtf2bed/.config.vsh.yaml

@@ -0,0 +1,156 @@
+name: "gtf2bed"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--gtf"
+    description: "A reference file in GTF format."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: " Output"
+  arguments:
+  - type: "file"
+    name: "--bed_output"
+    description: "BED file resulting from the conversion of the GTF input file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "gtf2bed.pl"
+description: "Create BED annotation file from GTF.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genes.gtf.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/gtf2bed.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+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: "apt"
+    packages:
+    - "perl"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/gtf2bed/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/gtf2bed"
+  executable: "target/executable/gtf2bed/gtf2bed"
+  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"

target/executable/gtf2bed/gtf2bed.pl

@@ -0,0 +1,122 @@
+#!/usr/bin/env perl
+
+# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
+
+use Getopt::Long;
+
+my $extended;
+GetOptions("x"=>\$extended);
+
+$in = shift @ARGV;
+
+my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n";
+open IN, $in_cmd;
+
+while (<IN>) {
+    $gff = 2 if /^##gff-version 2/;
+    $gff = 3 if /^##gff-version 3/;
+    next if /^#/ && $gff;
+
+    s/\s+$//;
+    # 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
+    my @f = split /\t/;
+    if ($gff) {
+        # most ver 2's stick gene names in the id field
+        ($id) = $f[8]=~ /\bID="([^"]+)"/;
+        # most ver 3's stick unquoted names in the name field
+        ($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
+    } else {
+        ($id) = $f[8]=~ /transcript_id "([^"]+)"/;
+    }
+
+    next unless $id && $f[0];
+
+    if ($f[2] eq 'exon') {
+        die "no position at exon on line $." if ! $f[3];
+        # gff3 puts :\d in exons sometimes
+        $id =~ s/:\d+$// if $gff == 3;
+        push @{$exons{$id}}, \@f;
+        # save lowest start
+        $trans{$id} = \@f if !$trans{$id};
+    } elsif ($f[2] eq 'start_codon') {
+        #optional, output codon start/stop as "thick" region in bed
+        $sc{$id}->[0] = $f[3];
+    } elsif ($f[2] eq 'stop_codon') {
+        $sc{$id}->[1] = $f[4];
+    } elsif ($f[2] eq 'miRNA' ) {
+        $trans{$id} = \@f if !$trans{$id};
+        push @{$exons{$id}}, \@f;
+    }
+}
+
+for $id (
+    # sort by chr then pos
+    sort {
+        $trans{$a}->[0] eq $trans{$b}->[0] ?
+        $trans{$a}->[3] <=> $trans{$b}->[3] :
+        $trans{$a}->[0] cmp $trans{$b}->[0]
+    } (keys(%trans)) ) {
+        my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
+        my ($cds, $cde);
+        ($cds, $cde) = @{$sc{$id}} if $sc{$id};
+
+        # sort by pos
+        my @ex = sort {
+            $a->[3] <=> $b->[3]
+        } @{$exons{$id}};
+
+        my $beg = $ex[0][3];
+        my $end = $ex[-1][4];
+
+        if ($dir eq '-') {
+            # swap
+            $tmp=$cds;
+            $cds=$cde;
+            $cde=$tmp;
+            $cds -= 2 if $cds;
+            $cde += 2 if $cde;
+        }
+
+        # not specified, just use exons
+        $cds = $beg if !$cds;
+        $cde = $end if !$cde;
+
+        # adjust start for bed
+        --$beg; --$cds;
+
+        my $exn = @ex;												# exon count
+        my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
+        my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
+
+        my $gene_id;
+        my $extend = "";
+        if ($extended) {
+            ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+            ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+            $extend="\t$gene_id";
+        }
+        # added an extra comma to make it look exactly like ucsc's beds
+        print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+}
+
+close IN;

target/executable/gtf_filter/.config.vsh.yaml

@@ -0,0 +1,166 @@
+name: "gtf_filter"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--fasta"
+    description: "Genome fasta file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "GTF file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--skip_transcript_id_check"
+    description: "Skip checking for transcript IDs in the GTF file."
+    info: null
+    direction: "input"
+- name: " Output"
+  arguments:
+  - type: "file"
+    name: "--filtered_gtf"
+    description: "Filtered GTF file containing only sequences in the FASTA file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+description: "Filters a GTF file based on sequence names in a FASTA file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genome.fasta"
+- type: "file"
+  path: "genes.gtf.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/gtf_filter.nf"
+    last_sha: "1c6012ecbb087014ea4b8f0f3d39b874850277a8"
+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: "python"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/gtf_filter/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/gtf_filter"
+  executable: "target/executable/gtf_filter/gtf_filter"
+  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"

target/executable/gunzip/.config.vsh.yaml

@@ -0,0 +1,155 @@
+name: "gunzip"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Path of file to be uncompressed"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Decompressed file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Compress or uncompress a file or list of files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genes.gff.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/gunzip/main.nf"
+    - "modules/nf-core/gunzip/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "gzip"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/gunzip/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/gunzip"
+  executable: "target/executable/gunzip/gunzip"
+  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"

target/executable/kallisto/kallisto_index/.config.vsh.yaml

@@ -0,0 +1,166 @@
+name: "kallisto_index"
+namespace: "kallisto"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--transcriptome_fasta"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--pseudo_aligner_kmer_size"
+    description: "Kmer length passed to indexing step of pseudoaligners."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--kallisto_index"
+    info: null
+    default:
+    - "Kallisto_index"
+    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: "Create Kallisto index.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "transcriptome.fasta"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/kallisto/index/main.nf"
+    - "modules/nf-core/kallisto/index/meta.yml"
+    last_sha: "c0816976384d5e7ee6079c29c45958df1ffa0ee4"
+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 --no-install-recommends wget && \\\
+      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
+      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/kallisto/kallisto_index/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/kallisto/kallisto_index"
+  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
+  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"

target/executable/kallisto/kallisto_quant/.config.vsh.yaml

@@ -0,0 +1,264 @@
+name: "kallisto_quant"
+namespace: "kallisto"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "List of input FastQ files of size 1 and 2 for single-end and paired-end\
+      \ data, respectively."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired reads or not."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index"
+    description: "Kallisto genome index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Optional gtf file for translation of transcripts into genomic coordinates."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--chromosomes"
+    description: "Optional tab separated file with chromosome names and lengths."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--fragment_length"
+    description: "For single-end mode only, the estimated average fragment length."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--fragment_length_sd"
+    description: "For single-end mode only, the estimated standard deviation of the\
+      \ fragment length."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Kallisto quant results"
+    info: null
+    default:
+    - "$id.kallisto_quant_results"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--log"
+    description: "File containing log information from running kallisto quant"
+    info: null
+    default:
+    - "$id.kallisto_quant.log.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--run_info"
+    description: "A json file containing information about the run"
+    info: null
+    default:
+    - "$id.run_info.json"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--quant_results_file"
+    description: "TSV file containing abundance estimates from Kallisto"
+    info: null
+    default:
+    - "$id.abundance.tsv"
+    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: "Computes equivalence classes for reads and quantifies abundances.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "transcriptome.fasta"
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/kallisto/quant/main.nf"
+    - "modules/nf-core/kallisto/quant/meta.yml"
+    last_sha: "aff1d2e02717247831644769fc3ba84868c3fdde"
+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 --no-install-recommends wget && \\\
+      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
+      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/kallisto/kallisto_quant/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/kallisto/kallisto_quant"
+  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
+  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"

target/executable/multiqc_custom_biotype/.config.vsh.yaml

@@ -0,0 +1,181 @@
+name: "multiqc_custom_biotype"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--biocounts"
+    description: "File with all biocounts"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--id"
+    description: "Sample name"
+    info: null
+    default:
+    - "$id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--biotypes_header"
+    info: null
+    default:
+    - "assets/multiqc/biotypes_header.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--featurecounts_multiqc"
+    info: null
+    default:
+    - "$id.biotype_counts_mqc.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--featurecounts_rrna_multiqc"
+    info: null
+    default:
+    - "$id.biotype_counts_rrna_mqc.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "mqc_features_stat.py"
+description: "Calculate features percentage for biotype counts"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "pip"
+    interactive: false
+  - type: "python"
+    user: false
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/multiqc_custom_biotype/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/multiqc_custom_biotype"
+  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
+  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"

target/executable/multiqc_custom_biotype/mqc_features_stat.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python3
+
+import argparse
+import logging
+import os
+
+# Create a logger
+logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
+logger = logging.getLogger(__file__)
+logger.setLevel(logging.INFO)
+
+mqc_main = """#id: 'biotype-gs'
+#plot_type: 'generalstats'
+#pconfig:"""
+
+mqc_pconf = """#    percent_{ft}:
+#        title: '% {ft}'
+#        namespace: 'Biotype Counts'
+#        description: '% reads overlapping {ft} features'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+#        format: '{{:.2f}}%'"""
+
+
+def mqc_feature_stat(bfile, features, outfile, sname=None):
+    # If sample name not given use file name
+    if not sname:
+        sname = os.path.splitext(os.path.basename(bfile))[0]
+
+    # Try to parse and read biocount file
+    fcounts = {}
+    try:
+        with open(bfile, "r") as bfl:
+            for ln in bfl:
+                if ln.startswith("#"):
+                    continue
+                ft, cn = ln.strip().split("\t")
+                fcounts[ft] = float(cn)
+    except:
+        logger.error("Trouble reading the biocount file {}".format(bfile))
+        return
+
+    total_count = sum(fcounts.values())
+    if total_count == 0:
+        logger.error("No biocounts found, exiting")
+        return
+
+    # Calculate percentage for each requested feature
+    fpercent = {f: (fcounts[f] / total_count) * 100 if f in fcounts else 0 for f in features}
+    if len(fpercent) == 0:
+        logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
+        return
+
+    # Prepare the output strings
+    out_head, out_value, out_mqc = ("Sample", "'{}'".format(sname), mqc_main)
+    for ft, pt in fpercent.items():
+        out_head = "{}\tpercent_{}".format(out_head, ft)
+        out_value = "{}\t{}".format(out_value, pt)
+        out_mqc = "{}\n{}".format(out_mqc, mqc_pconf.format(ft=ft))
+
+    # Write the output to a file
+    with open(outfile, "w") as ofl:
+        out_final = "\n".join([out_mqc, out_head, out_value]).strip()
+        ofl.write(out_final + "\n")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="""Calculate features percentage for biotype counts""")
+    parser.add_argument("biocount", type=str, help="File with all biocounts")
+    parser.add_argument(
+        "-f",
+        "--features",
+        dest="features",
+        required=True,
+        nargs="+",
+        help="Features to count",
+    )
+    parser.add_argument("-s", "--sample", dest="sample", type=str, help="Sample Name")
+    parser.add_argument(
+        "-o",
+        "--output",
+        dest="output",
+        default="biocount_percent.tsv",
+        type=str,
+        help="Sample Name",
+    )
+    args = parser.parse_args()
+    mqc_feature_stat(args.biocount, args.features, args.output, args.sample)

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"

target/executable/prepare_multiqc_input/.config.vsh.yaml

@@ -0,0 +1,420 @@
+name: "prepare_multiqc_input"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--fail_trimming_multiqc"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--fail_mapping_multiqc"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--fail_strand_multiqc"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_raw_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--fastqc_trim_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--trim_log_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--sortmerna_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--star_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--salmon_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--samtools_stats"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--samtools_flagstat"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--samtools_idxstats"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--markduplicates_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--pseudo_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--featurecounts_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--featurecounts_rrna_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--aligner_pca_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--aligner_clustering_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--pseudo_aligner_pca_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--pseudo_aligner_clustering_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--preseq_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--qualimap_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--dupradar_output_dup_intercept_mqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--dupradar_output_duprate_exp_denscurve_mqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--bamstat_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--inferexperiment_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--innerdistance_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--junctionannotation_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--junctionsaturation_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--readdistribution_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--readduplication_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--tin_multiqc"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--multiqc_config"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Ouput"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "multiqc_input"
+    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: "Prepare directory with all the input files for MultiQC.\n"
+info: null
+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: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/prepare_multiqc_input/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/prepare_multiqc_input"
+  executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
+  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"

target/executable/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -0,0 +1,149 @@
+name: "preprocess_transcripts_fasta"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--transcript_fasta"
+    description: "Path of transcripts FASTA file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Path of processed output FASTA file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Process transcripts FASTA if GTF file is GENOCODE format\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "transcriptome.fasta"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/preprocess_transcripts_fasta_gencode.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+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: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/preprocess_transcripts_fasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/preprocess_transcripts_fasta"
+  executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
+  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"

target/executable/preseq_lcextrap/.config.vsh.yaml

@@ -0,0 +1,202 @@
+name: "preseq_lcextrap"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input genome BAM/BED file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_preseq_args"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired-end reads?"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "$id.lc_extrap.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Computing the expected future yield of distinct reads and bounds on\
+  \ the number of total distinct reads in the library and the associated confidence\
+  \ intervals."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "a.sorted.bed"
+- type: "file"
+  path: "SRR1106616_5M_subset.bam"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/preseq/lcextrap/main.nf"
+    - "modules/nf-core/preseq/lcextrap/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "curl"
+    - "bzip2"
+    - "build-essential"
+    - "wget"
+    - "gcc"
+    - "autoconf"
+    - "automake"
+    - "make"
+    - "libz-dev"
+    - "libbz2-dev"
+    - "zlib1g-dev"
+    - "libncurses5-dev"
+    - "libncursesw5-dev"
+    - "liblzma-dev"
+    - "pip"
+    interactive: false
+  - type: "docker"
+    run:
+    - "cd /usr/bin && \\\nwget --no-check-certificate https://github.com/smithlabcode/preseq/releases/download/v3.2.0/preseq-3.2.0.tar.gz\
+      \ && \\\nwget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2\
+      \ && \\\nwget --no-check-certificate https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static\
+      \ && \\\ncurl -fsSL https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2\
+      \ -o samtools-1.18.tar.bz2 && \\\ntar -xjf samtools-1.18.tar.bz2 && rm samtools-1.18.tar.bz2\
+      \ && \\\ntar -xzf preseq-3.2.0.tar.gz && rm preseq-3.2.0.tar.gz && \\\ntar -vxjf\
+      \ htslib-1.9.tar.bz2 && rm htslib-1.9.tar.bz2 && \\\nmv bedtools.static /usr/local/bin/bedtools\
+      \ && \\\nchmod a+x /usr/local/bin/bedtools && \\\ncd samtools-1.18 && \\\n./configure\
+      \ && \\\nmake && \\\nmake install && \\\ncd /usr/bin && cd htslib-1.9 && \\\n\
+      make && \\\ncd /usr/bin && cd preseq-3.2.0 && \\\nmkdir build && cd build &&\
+      \ \\\n../configure && \\\nmake && make install && make HAVE_HTSLIB=1 all \n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/preseq_lcextrap/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/preseq_lcextrap"
+  executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
+  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"

target/executable/qualimap/.config.vsh.yaml

@@ -0,0 +1,282 @@
+name: "qualimap"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "path to input mapping file in BAM format."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "path to annotations file in Ensembl GTF format."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_dir"
+    description: "path to output directory for raw data and report."
+    info: null
+    default:
+    - "$id.qualimap_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_pdf"
+    description: "path to output file for pdf report."
+    info: null
+    default:
+    - "$id.report.pdf"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_format"
+    description: "Format of the output report (PDF or HTML, default is HTML)"
+    info: null
+    default:
+    - "html"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Optional"
+  arguments:
+  - type: "integer"
+    name: "--pr_bases"
+    description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
+      \ bias (default = 100)."
+    info: null
+    default:
+    - 100
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--tr_bias"
+    description: "Number of top highly expressed transcripts to compute 5'-3' bias\
+      \ (default = 1000)."
+    info: null
+    default:
+    - 1000
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--algorithm"
+    description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
+    info: null
+    default:
+    - "uniquely-mapped-reads"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--sequencing_protocol"
+    description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
+      \ or non-strand-specific (default))."
+    info: null
+    default:
+    - "non-strand-specific"
+    required: false
+    choices:
+    - "non-strand-specific"
+    - "strand-specific-reverse"
+    - "strand-specific-forward"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--paired"
+    description: "Setting this flag for paired-end experiments will result in counting\
+      \ fragments instead of reads."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sorted"
+    description: "Setting this flag indicates that the input file is already sorted\
+      \ by name. If flag is not set, additional sorting by name will be performed.\
+      \ Only requiredfor paired-end analysis."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--java_memory_size"
+    description: "maximum Java heap memory size, default = 4G."
+    info: null
+    default:
+    - "4G"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "RNA-seq QC analysis using the qualimap \n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam"
+- type: "file"
+  path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai"
+- type: "file"
+  path: "genes.gtf"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/qualimap/rnaseq/main.nf"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "r-base"
+    - "unzip"
+    - "wget"
+    - "openjdk-8-jdk"
+    - "libxml2-dev"
+    - "libcurl4-openssl-dev"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip &&\
+      \ \\\nunzip qualimap_v2.3.zip && \\\ncp -a qualimap_v2.3/. usr/bin && \\\nunset\
+      \ DISPLAY && \\\nmkdir -p tmp && \\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp\n"
+  - type: "r"
+    cran:
+    - "optparse"
+    bioc:
+    - "NOISeqr"
+    bioc_force_install: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/qualimap/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/qualimap"
+  executable: "target/executable/qualimap/qualimap"
+  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"

target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml

@@ -0,0 +1,319 @@
+name: "rsem_calculate_expression"
+namespace: "rsem"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "Sample ID."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
+    info: null
+    required: false
+    choices:
+    - "forward"
+    - "reverse"
+    - "unstranded"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired-end reads or not?"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Input reads for quantification."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--index"
+    description: "RSEM index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_args"
+    description: "Extra rsem-calculate-expression arguments in addition to the defaults."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--versions"
+    info: null
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--counts_gene"
+    description: "Expression counts on gene level"
+    info: null
+    example:
+    - "sample.genes.results"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_transcripts"
+    description: "Expression counts on transcript level"
+    info: null
+    example:
+    - "sample.isoforms.results"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--stat"
+    description: "RSEM statistics"
+    info: null
+    example:
+    - "sample.stat"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--logs"
+    description: "RSEM logs"
+    info: null
+    example:
+    - "sample.log"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bam_star"
+    description: "BAM file generated by STAR (optional)"
+    info: null
+    example:
+    - "sample.STAR.genome.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bam_genome"
+    description: "Genome BAM file (optional)"
+    info: null
+    example:
+    - "sample.genome.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bam_transcript"
+    description: "Transcript BAM file (optional)"
+    info: null
+    example:
+    - "sample.transcript.bam"
+    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: "Calculate expression with RSEM.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+- type: "file"
+  path: "rsem.tar.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rsem/calculateexpression/main.nf"
+    - "modules/nf-core/rsem/calculateexpression/meta.yml"
+    last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
+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: "apt"
+    packages:
+    - "build-essential"
+    - "gcc"
+    - "g++"
+    - "make"
+    - "wget"
+    - "zlib1g-dev"
+    - "unzip"
+    - "xxd"
+    - "perl"
+    - "r-base"
+    - "bowtie2"
+    - "python3-pip"
+    - "git"
+    interactive: false
+  - type: "docker"
+    run:
+    - "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
+      \ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip\
+      \ && \\\nunzip ${STAR_VERSION}.zip && \\\ncd STAR-${STAR_VERSION}/source &&\
+      \ \\\nmake STARstatic CXXFLAGS_SIMD=-std=c++11 && \\\ncp STAR /usr/local/bin\
+      \ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip\
+      \ && \\\nunzip v${RSEM_VERSION}.zip && \\\ncd RSEM-${RSEM_VERSION} && \\\nmake\
+      \ && \\\nmake install && \\\nrm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip\
+      \ && \\\nrm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \\\n\
+      cd && \\\napt-get clean && \\\necho 'export PATH=$PATH:/usr/local/bin' >> /etc/profile\
+      \ && \\\necho 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \\\n/bin/bash\
+      \ -c \"source /etc/profile && source ~/.bashrc && echo $PATH && which STAR\"\
+      \n"
+    env:
+    - "STAR_VERSION=2.7.11b"
+    - "RSEM_VERSION=1.3.3"
+    - "TZ=Europe/Brussels"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rsem/rsem_calculate_expression/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rsem/rsem_calculate_expression"
+  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+package_config:
+  version: "main"
+  info:
+    test_resources:
+    - path: "gs://viash-hub-test-data/rnaseq/v1"
+      dest: "testData"
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  organization: "vsh"

target/executable/rsem/rsem_merge_counts/.config.vsh.yaml

@@ -0,0 +1,213 @@
+name: "rsem_merge_counts"
+namespace: "rsem"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--counts_gene"
+    description: "Expression counts on gene level (genes)"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_transcripts"
+    description: "Expression counts on transcript level (isoforms)"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--versions"
+    info: null
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--merged_gene_counts"
+    description: "File containing gene counts across all samples."
+    info: null
+    default:
+    - "rsem.merged.gene_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--merged_gene_tpm"
+    description: "File containing gene TPM across all samples."
+    info: null
+    default:
+    - "rsem.merged.gene_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--merged_transcript_counts"
+    description: "File containing transcript counts across all samples."
+    info: null
+    default:
+    - "rsem.merged.transcript_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--merged_transcript_tpm"
+    description: "File containing transcript TPM across all samples."
+    info: null
+    default:
+    - "rsem.merged.transcript_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--updated_versions"
+    info: null
+    default:
+    - "versions.yml"
+    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: "Merge the transcript quantification results obtained from rsem calculate-expression\
+  \ across all samples.\n"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/rsem_merge_counts/main.nf"
+    last_sha: "311279532694ce7520164ce4d65a388c0cd11f60"
+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: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rsem/rsem_merge_counts/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rsem/rsem_merge_counts"
+  executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
+  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"

target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml

@@ -0,0 +1,174 @@
+name: "rseqc_bamstat"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output file (txt) with mapping quality statistics"
+    info: null
+    default:
+    - "$id.mapping_quality.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Generate statistics from a bam file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/bamstat/main.nf"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "python3-pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_bamstat/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_bamstat"
+  executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
+  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"

target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml

@@ -0,0 +1,197 @@
+name: "rseqc_inferexperiment"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "Reference gene model in bed format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sample_size"
+    description: "Numer of reads sampled from SAM/BAM file, default = 200000."
+    info: null
+    default:
+    - 200000
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output file (txt) of strandness report"
+    info: null
+    default:
+    - "$id.strandedness.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Infer strandedness from sequencing reads\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.bed12"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/inferexperiment/main.nf"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "python3-pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_inferexperiment/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_inferexperiment"
+  executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
+  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"

target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml

@@ -0,0 +1,283 @@
+name: "rseqc_innerdistance"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "Reference gene model in bed format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sample_size"
+    description: "Numer of reads sampled from SAM/BAM file, default = 200000."
+    info: null
+    default:
+    - 200000
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--lower_bound_size"
+    description: "Lower bound of inner distance (bp). This option is used for ploting\
+      \ histograme, default=-250."
+    info: null
+    default:
+    - -250
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--upper_bound_size"
+    description: "Upper bound of inner distance (bp). This option is used for ploting\
+      \ histograme, default=250."
+    info: null
+    default:
+    - 250
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--step_size"
+    description: "Step size (bp) of histograme. This option is used for plotting histogram,\
+      \ default=5."
+    info: null
+    default:
+    - 5
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_stats"
+    description: "output file (txt) with summary statistics of inner distances of\
+      \ paired reads"
+    info: null
+    default:
+    - "$id.inner_distance.stats"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_dist"
+    description: "output file (txt) with inner distances of all paired reads"
+    info: null
+    default:
+    - "$id.inner_distance.txt"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_freq"
+    description: "output file (txt) with frequencies of inner distances of all paired\
+      \ reads"
+    info: null
+    default:
+    - "$id.inner_distance_freq.txt"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plot"
+    description: "output file (pdf) with histogram plot of of inner distances of all\
+      \ paired reads"
+    info: null
+    default:
+    - "$id.inner_distance_plot.pdf"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plot_r"
+    description: "output file (R) with script of histogram plot of of inner distances\
+      \ of all paired reads"
+    info: null
+    default:
+    - "$id.inner_distance_plot.r"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Calculate inner distance between read pairs. \n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.bed12"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/innerdistance/main.nf"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "python3-pip"
+    - "r-base"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_innerdistance/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_innerdistance"
+  executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
+  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"

target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml

@@ -0,0 +1,271 @@
+name: "rseqc_junctionannotation"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "Reference gene model in bed format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_intron"
+    description: "Minimum intron length (bp), default = 50."
+    info: null
+    default:
+    - 50
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_log"
+    description: "output log of junction annotation script"
+    info: null
+    default:
+    - "$id.junction_annotation.log"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plot_r"
+    description: "r script to generate splice_junction and splice_events plot"
+    info: null
+    default:
+    - "$id.junction_annotation_plot.r"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_junction_bed"
+    description: "junction annotation file (bed format)"
+    info: null
+    default:
+    - "$id.junction_annotation.bed"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_junction_interact"
+    description: "interact file (bed format) of junctions. Can be uploaded to UCSC\
+      \ genome browser or converted to bigInteract (using bedToBigBed program) for\
+      \ visualization."
+    info: null
+    default:
+    - "$id.junction_annotation.Interact.bed"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_junction_sheet"
+    description: "junction annotation file (xls format)"
+    info: null
+    default:
+    - "$id.junction_annotation.xls"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_splice_events_plot"
+    description: "plot of splice events (pdf)"
+    info: null
+    default:
+    - "$id.splice_events.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_splice_junctions_plot"
+    description: "plot of junctions (pdf)"
+    info: null
+    default:
+    - "$id.splice_junctions_plot.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Compare detected splice junctions to reference gene model.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.bed12"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/junctionannotation/main.nf"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "python3-pip"
+    - "r-base"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_junctionannotation/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_junctionannotation"
+  executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
+  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"

target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml

@@ -0,0 +1,260 @@
+name: "rseqc_junctionsaturation"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "Reference gene model in bed format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sampling_percentile_lower_bound"
+    description: "Sampling starts from this percentile, must be an integer between\
+      \ 0 and 100, default =5."
+    info: null
+    default:
+    - 5
+    required: false
+    min: 0
+    max: 100
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sampling_percentile_upper_bound"
+    description: "Sampling ends at this percentile, must be an integer between 0 and\
+      \ 100, default =5."
+    info: null
+    default:
+    - 100
+    required: false
+    min: 0
+    max: 100
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sampling_percentile_step"
+    description: "Sampling frequency in %. Smaller value means more sampling times.\
+      \ Must be an integer between 0 and 100, default = 5."
+    info: null
+    default:
+    - 5
+    required: false
+    min: 0
+    max: 100
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_intron"
+    description: "Minimum intron length (bp), default = 50."
+    info: null
+    default:
+    - 50
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_splice_read"
+    description: "Minimum number of supporting reads to call a junction, default =\
+      \ 1."
+    info: null
+    default:
+    - 1
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_plot_r"
+    description: "r script to generate junction_saturation_plot plot"
+    info: null
+    default:
+    - "$id.junction_saturation_plot.r"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plot"
+    description: "plot of junction saturation (pdf)"
+    info: null
+    default:
+    - "$id.junction_saturation_plot.pdf"
+    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: "Compare detected splice junctions to reference gene model.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.bed"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/junctionsaturation/main.nf"
+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: "apt"
+    packages:
+    - "python3-pip"
+    - "r-base"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_junctionsaturation/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_junctionsaturation"
+  executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
+  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"

target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml

@@ -0,0 +1,173 @@
+name: "rseqc_readdistribution"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "Reference gene model in bed format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output file (txt) of read distribution analysis."
+    info: null
+    default:
+    - "$id.read_distribution.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Calculate how mapped reads are distributed over genomic features.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.bed12"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/readdistribution/main.nf"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "python3-pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_readdistribution/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_readdistribution"
+  executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
+  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"

target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml

@@ -0,0 +1,222 @@
+name: "rseqc_readduplication"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input alignment file in BAM or SAM format"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--read_count_upper_limit"
+    description: "Upper limit of reads' occurence. Only used for plotting, default\
+      \ = 500 (times)."
+    info: null
+    default:
+    - 500
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--map_qual"
+    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
+      \ reads, default=30."
+    info: null
+    default:
+    - 30
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_duplication_rate_plot_r"
+    description: "R script for generating duplication rate plot"
+    info: null
+    default:
+    - "$id.duplication_rate_plot.r"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duplication_rate_plot"
+    description: "duplication rate plot (pdf)"
+    info: null
+    default:
+    - "$id.duplication_rate_plot.pdf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duplication_rate_mapping"
+    description: "Summary of mapping-based read duplication"
+    info: null
+    default:
+    - "$id.duplication_rate_mapping.xls"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_duplication_rate_sequence"
+    description: "Summary of sequencing-based read duplication"
+    info: null
+    default:
+    - "$id.duplication_rate_sequencing.xls"
+    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: "Calculate read duplication rate.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/readduplication/main.nf"
+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: "apt"
+    packages:
+    - "python3-pip"
+    - "r-base"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "RSeQC"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/rseqc_readduplication/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_readduplication"
+  executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
+  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"

target/executable/rseqc/rseqc_tin/.config.vsh.yaml

@@ -0,0 +1,225 @@
+name: "rseqc_tin"
+namespace: "rseqc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bam_input"
+    description: "Path to input alignment file in BAM or SAM format."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bai_input"
+    description: "Path to bam index file in bai format."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refgene"
+    description: "BED file containing the reference gene model"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--minimum_coverage"
+    description: "Minimum number of reads mapped to a transcript, default = 10."
+    info: null
+    default:
+    - 10
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sample_size"
+    description: "Number of equal-spaced nucleotide positions picked from mRNA. Note,\
+      \ if this number is larger than the length of mRNA (L), it will be halved until\
+      \ it's smaller than L (default = 100)"
+    info: null
+    default:
+    - 100
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--subtract_background"
+    description: "Set flag to subtract background noise (estimated from intronic reads).\
+      \ Only use this option if there are substantial intronic reads."
+    info: null
+    direction: "input"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_tin_summary"
+    description: "summary statistics (txt) of calculated TIN metrics"
+    info: null
+    default:
+    - "$id.tin_summary.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_tin"
+    description: "file with TIN metrics (xls)"
+    info: null
+    default:
+    - "$id.tin.xls"
+    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: "Calculte TIN (transcript integrity number) from RNA-seq reads\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.paired_end.sorted.bam"
+- type: "file"
+  path: "test.paired_end.sorted.bam.bai"
+- type: "file"
+  path: "test.bed12"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/rseqc/tin/main.nf"
+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: "apt"
+    packages:
+    - "python3-pip"
+    interactive: false
+  - type: "docker"
+    run:
+    - "pip3 install RSeQC\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/rseqc/tin/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/rseqc/rseqc_tin"
+  executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
+  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"

target/executable/sortmerna/.config.vsh.yaml

@@ -0,0 +1,209 @@
+name: "sortmerna"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "boolean"
+    name: "--paired"
+    description: "Are the reads single-end or paired-end"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--ribo_database_manifest"
+    description: "Text file containing paths to fasta files (one per line) that will\
+      \ be used to create the database for SortMeRNA."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--sortmerna_log"
+    description: "Sortmerna log file."
+    info: null
+    default:
+    - "$id.sortmerna.log"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_1"
+    description: "Output file for read 1."
+    info: null
+    default:
+    - "$id.$key.read_1.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Output file for read 2."
+    info: null
+    default:
+    - "$id.$key.read_2.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Local sequence alignment tool for filtering, mapping and clustering.\
+  \ The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.\
+  \ SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and\
+  \ one or multiple rRNA database file(s), and sorts apart aligned and rejected reads\
+  \ into two files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "SRR6357070_1.fastq.gz"
+- type: "file"
+  path: "SRR6357070_2.fastq.gz"
+- type: "file"
+  path: "rRNA"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/sortmerna/main.nf"
+    - "modules/nf-core/sortmerna/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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 --no-install-recommends cmake g++\
+      \ wget && \\\napt-get clean && \\\nwget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/download/v4.3.6/sortmerna-4.3.6-Linux.sh\
+      \ && \\\nbash sortmerna-4.3.6-Linux.sh --skip-license\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/sortmerna/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/sortmerna"
+  executable: "target/executable/sortmerna/sortmerna"
+  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"

target/executable/stringtie/.config.vsh.yaml

@@ -0,0 +1,227 @@
+name: "stringtie"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--strandedness"
+    description: "Forward or reverse strand?"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bam"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--annotation_gtf"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_stringtie_args"
+    description: "Extra arguments for running StringTie"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--stringtie_ignore_gtf"
+    description: "Perform reference-guided de novo assembly of transcripts using StringTie,\
+      \ i.e. don't restrict to those in GTF file."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--transcript_gtf"
+    info: null
+    default:
+    - "$id.$key.transcripts.gtf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--coverage_gtf"
+    info: null
+    default:
+    - "$id.$key.coverage.gtf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--abundance"
+    info: null
+    default:
+    - "$id.$key.abundance.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ballgown"
+    description: "for running ballgown"
+    info: null
+    default:
+    - "$id.$key.ballgown"
+    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: "Transcript assembly and quantification for RNA-Seq\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "genes.gtf"
+- type: "file"
+  path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/stringtie/stringtie/main.nf"
+    - "modules/nf-core/stringtie/stringtie/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 zlib1g wget && \\\n\
+      wget --no-check-certificate https://github.com/gpertea/stringtie/releases/download/v2.2.1/stringtie-2.2.1.Linux_x86_64.tar.gz\
+      \ && \\\ntar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \\\ncp stringtie-2.2.1.Linux_x86_64/stringtie\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/stringtie/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/stringtie"
+  executable: "target/executable/stringtie/stringtie"
+  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"

target/executable/summarizedexperiment/.config.vsh.yaml

@@ -0,0 +1,210 @@
+name: "summarizedexperiment"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--tpm_gene"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_length_scaled"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_scaled"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tpm_transcript"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_transcript"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tx2gene_tsv"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "merged_summarizedexperiment"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "summarizedexperiment.r"
+description: "Create SummarizedExperiment object from Salmon counts"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/summarizedexperiment/main.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+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: "apt"
+    packages:
+    - "r-base"
+    - "libcurl4-openssl-dev"
+    interactive: false
+  - type: "r"
+    bioc:
+    - "SummarizedExperiment"
+    - "tximeta"
+    bioc_force_install: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/summarizedexperiment/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/summarizedexperiment"
+  executable: "target/executable/summarizedexperiment/summarizedexperiment"
+  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"

target/executable/summarizedexperiment/summarizedexperiment.r

@@ -0,0 +1,68 @@
+#!/usr/bin/env Rscript
+
+library(SummarizedExperiment)
+
+## Create SummarizedExperiment (se) object from Salmon counts
+
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) < 2) {
+    stop("Usage: salmon_se.r <coldata> <counts> <tpm>", call. = FALSE)
+}
+
+coldata <- args[1]
+counts_fn <- args[2]
+tpm_fn <- args[3]
+tx2gene <- args[4]
+
+info <- file.info(tx2gene)
+if (info$size == 0) {
+    tx2gene <- NULL
+} else {
+    rowdata <- read.csv(tx2gene, sep = "\t", header = FALSE)
+    colnames(rowdata) <- c("tx", "gene_id", "gene_name")
+    tx2gene <- rowdata[, 1:2]
+}
+
+counts <- read.csv(counts_fn, row.names = 1, sep = "\t")
+counts <- counts[, 2:ncol(counts), drop = FALSE] # remove gene_name column
+tpm <- read.csv(tpm_fn, row.names = 1, sep = "\t")
+tpm <- tpm[, 2:ncol(tpm), drop = FALSE] # remove gene_name column
+
+if (length(intersect(rownames(counts), rowdata[["tx"]])) > length(intersect(rownames(counts), rowdata[["gene_id"]]))) {
+    by_what <- "tx"
+} else {
+    by_what <- "gene_id"
+    rowdata <- unique(rowdata[, 2:3])
+}
+
+if (file.exists(coldata)) {
+    coldata <- read.csv(coldata, sep = "\t")
+    coldata <- coldata[match(colnames(counts), coldata[, 1]), ]
+    coldata <- cbind(files = fns, coldata)
+} else {
+    message("ColData not avaliable ", coldata)
+    coldata <- data.frame(files = colnames(counts), names = colnames(counts))
+}
+
+rownames(coldata) <- coldata[["names"]]
+extra <- setdiff(rownames(counts), as.character(rowdata[[by_what]]))
+if (length(extra) > 0) {
+    rowdata <- rbind(
+        rowdata,
+        data.frame(
+            tx = extra,
+            gene_id = extra,
+            gene_name = extra
+        )[, colnames(rowdata)]
+    )
+}
+
+rowdata <- rowdata[match(rownames(counts), as.character(rowdata[[by_what]])), ]
+rownames(rowdata) <- rowdata[[by_what]]
+se <- SummarizedExperiment(
+    assays = list(counts = counts, abundance = tpm),
+    colData = DataFrame(coldata),
+    rowData = rowdata
+)
+
+saveRDS(se, file = paste0(tools::file_path_sans_ext(counts_fn), ".rds")) 

target/executable/trimgalore/.config.vsh.yaml

@@ -0,0 +1,799 @@
+name: "trimgalore"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input files. Note that paired-end files need to be supplied in a\
+      \ pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz"
+    info: null
+    example:
+    - "sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Trimming options"
+  arguments:
+  - type: "integer"
+    name: "--quality"
+    alternatives:
+    - "-q"
+    description: "Trim low-quality ends (below the specified Phred score) from reads\
+      \ in addition to adapter removal. For RRBS samples, quality trimming will be\
+      \ performed first, and adapter trimming is carried in a second round. Other\
+      \ files are quality and adapter trimmed in a single pass. The algorithm is the\
+      \ same as the one used by BWA (Subtract INT from all qualities; compute partial\
+      \ sums from all indices to the end of the sequence; cut sequence at the index\
+      \ at which the sum is minimal)."
+    info: null
+    example:
+    - 20
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--phred33"
+    description: "Instructs Cutadapt to use ASCII+33 quality scores as Phred scores\
+      \ (Sanger/Illumina 1.9+ encoding) for quality trimming."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--phred64"
+    description: "Instructs Cutadapt to use ASCII+64 quality scores as Phred scores\
+      \ (Illumina 1.5 encoding) for quality trimming."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--fastqc"
+    description: "Run FastQC in the default mode on the FastQ file once trimming is\
+      \ complete."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--fastqc_args"
+    description: "Passes extra arguments to FastQC. If more than one argument is to\
+      \ be passed to FastQC they must be in the form \"arg1 arg2 ...\". Passing extra\
+      \ arguments will automatically invoke FastQC, so --fastqc does not have to be\
+      \ specified separately."
+    info: null
+    example:
+    - "--nogroup --outdir /home/"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--adapter"
+    alternatives:
+    - "-a"
+    description: "Adapter sequence to be trimmed. If not specified explicitly, Trim\
+      \ Galore will try to auto-detect whether the Illumina universal, Nextera transposase\
+      \ or Illumina small RNA adapter sequence was used. A single base may also be\
+      \ given as e.g. -a A{10}, to be expanded to -a AAAAAAAAAA. \nAt a special request,\
+      \ multiple adapters can also be specified like so: \n  -a  \" AGCTCCCG -a TTTCATTATAT\
+      \ -a TTTATTCGGATTTAT\" -a2 \" AGCTAGCG -a TCTCTTATAT -a TTTCGGATTTAT\", \nor\
+      \ so:\n  -a \"file:../multiple_adapters.fa\" -a2 \"file:../different_adapters.fa\"\
+      \nPotentially in conjucntion with the parameter \"-n 3\" to trim all adapters.\
+      \ \n      example: 20\n"
+    info: null
+    example:
+    - "AGCTCCCG"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--adapter2"
+    alternatives:
+    - "-a2"
+    description: "Optional adapter sequence to be trimmed off read 2 of paired-end\
+      \ files. This option requires '--paired' to be specified as well. If the libraries\
+      \ to be trimmed are smallRNA then a2 will be set to the Illumina small RNA 5'\
+      \ adapter automatically (GATCGTCGGACT). A single base may also be given as e.g.\
+      \ -a2 A{10}, to be expanded to -a2 AAAAAAAAAA."
+    info: null
+    example:
+    - "AGCTCCCG"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--illumina"
+    description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
+      \ universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of\
+      \ adapter sequence."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--stranded_illumina"
+    description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
+      \ stranded mRNA or Total RNA adapter 'ACTGTCTCTTATA' instead of the default\
+      \ auto-detection of adapter sequence."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--nextera"
+    description: "Adapter sequence to be trimmed is the first 12bp of the Nextera\
+      \ adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--small_rna"
+    description: "Adapter sequence to be trimmed is the first 12bp of the Illumina\
+      \ Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection\
+      \ of adapter sequence. Selecting to trim smallRNA adapters will also lower the\
+      \ --length value to 18bp. If the smallRNA libraries are paired-end then a automatically\
+      \ (GATCGTCGGACT) unless -a 2 had been defined explicitly."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--consider_already_trimmed"
+    description: "During adapter auto-detection, the limit set by this argument allows\
+      \ the user to set a threshold up to which the file is considered already adapter-trimmed.\
+      \ If no adapter sequence exceeds this threshold, no additional adapter trimming\
+      \ will be performed (technically, the adapter is set to '-a X'). Quality trimming\
+      \ is still performed as usual."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_length"
+    description: "Discard reads that are longer than the specified value after trimming.\
+      \ This is only advised for smallRNA sequencing to remove non-small RNA sequences."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--stringency"
+    description: "Overlap with adapter sequence required to trim a sequence. Defaults\
+      \ to a very stringent setting of 1, i.e. even a single bp of overlapping sequence\
+      \ will be trimmed off from the 3' end of any read."
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--error_rate"
+    alternatives:
+    - "-e"
+    description: "Maximum allowed error rate (no. of errors divided by the length\
+      \ of the matching region)"
+    info: null
+    example:
+    - 0.1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--gzip"
+    description: "Compress the output file with GZIP. If the input files are GZIP-compressed\
+      \ the output files will automatically be GZIP compressed as well. As of v0.2.8\
+      \ the compression will take place on the fly."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--dont_gzip"
+    description: "Output files won't be compressed with GZIP. This option overrides\
+      \ --gzip."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--length"
+    description: "Discard reads that became shorter than the specified length because\
+      \ of either quality or adapter trimming. A value of '0' effectively disables\
+      \ this behaviour. For paired-end files, both reads of a read-pair need to be\
+      \ longer than the specified length to be printed out to validated paired-end\
+      \ files. If only one read became too short there is the possibility of keeping\
+      \ such unpaired single-end reads using the --retain_unpaired option."
+    info: null
+    example:
+    - 20
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_n"
+    description: "The total number of Ns a read may contain before it will be removed\
+      \ altogether.In a paired-end setting, either read exceeding this limit will\
+      \ result in the entire pair being removed from the trimmed output files. If\
+      \ COUNT is a number between 0 and 1, it is interpreted as a fraction of the\
+      \ read length."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--trim_n"
+    description: "Removes Ns from either side of the read. This option does currently\
+      \ not work in RRBS mode."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--no_report_file"
+    description: "If specified no report file will be generated."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--suppress_warn"
+    description: "If specified any output to STDOUT or STDERR will be suppressed."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--clip_R1"
+    description: "Instructs TrimGalore to remove given number of bp from the 5' end\
+      \ of read 1 (or single-end reads). This may be useful if the qualities were\
+      \ very poor, or if there is some sort of unwanted bias at the 5' end."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--clip_R2"
+    description: "Instructs TrimGalore to remove given number bp from the 5' end of\
+      \ read 2 (paired-end reads only). This may be useful if the qualities were very\
+      \ poor, or if there is some sort of unwanted bias at the 5' end. For paired-end\
+      \ BS-Seq, it is recommended to remove the first few bp because the end-repair\
+      \ reaction may introduce a bias towards low methylation."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--three_prime_clip_R1"
+    description: "Instructs Trim Galore to remove spacified number of bp from the\
+      \ 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has\
+      \ been performed. This may remove some  bias from the 3' end that is not directly\
+      \ related to adapter sequence or basecall quality."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--three_prime_clip_R2"
+    description: "Instructs Trim Galore to remove <int> bp from the 3' end of read\
+      \ 2 AFTER adapter/quality trimming has been performed. This may remove some\
+      \ unwanted bias from the 3' end that is not directly related to adapter sequence\
+      \ or basecall quality."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--nextseq"
+    description: "This enables the option '--nextseq-trim=3'CUTOFF' within Cutadapt,\
+      \ which will set a quality cutoff (that is normally given with -q instead),\
+      \ but qualities of G bases are ignored. This trimming is in common for the NextSeq-\
+      \ and NovaSeq-platforms, where basecalls without any signal are called as high-quality\
+      \ G bases. This is mutually exlusive with '-q INT'."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--basename"
+    description: "Use specified name (PREFERRED_NAME) as the basename for output files,\
+      \ instead of deriving the filenames from the input files. Single-end data would\
+      \ be called PREFERRED_NAME_trimmed.fq(.gz), or PREFERRED_NAME_val_1.fq(.gz)\
+      \ and PREFERRED_NAME_val_2.fq(.gz) for paired-end data. --basename only works\
+      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
+      \ longer lists."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--cores"
+    alternatives:
+    - "-j"
+    description: "Number of cores to be used for trimming"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Specific trimming options without adapter/quality trimming"
+  arguments:
+  - type: "integer"
+    name: "--hardtrim5"
+    description: "Instead of performing adapter-/quality trimming, this option will\
+      \ simply hard-trim sequences to <int> bp at the 5'-end. Once hard-trimming of\
+      \ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
+      \ in .<int>_5prime.fq(.gz)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--hardtrim3"
+    description: "Instead of performing adapter-/quality trimming, this option will\
+      \ simply hard-trim sequences to <int> bp at the 3'-end. Once hard-trimming of\
+      \ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
+      \ in .<int>_3prime.fq(.gz)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--clock"
+    description: "In this mode, reads are trimmed in a specific way that is currently\
+      \ used for the Mouse Epigenetic Clock."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--polyA"
+    description: "This is a new, still experimental, trimming mode to identify and\
+      \ remove poly-A tails from sequences. When --polyA is selected, Trim Galore\
+      \ attempts to identify from the first supplied sample whether sequences contain\
+      \ more often a stretch of either 'AAAAAAAAAA' or 'TTTTTTTTTT'. This determines\
+      \ if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA\
+      \ or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary\
+      \ base from the start of the reads. The auto-detection uses a default of A{20}\
+      \ for Read1 (3'-end trimming) and T{150} for Read2 (5'-end trimming). These\
+      \ values may be changed manually using the options -a and -a2. In addition to\
+      \ trimming the sequences, white spaces are replaced with _ and it records in\
+      \ the read ID how many bases were trimmed so it can later be used to identify\
+      \ PolyA trimmed sequences. This is currently done by writing tags to both the\
+      \ start (\"32:A:\") and end (\"_PolyA:32\") of the reads. The poly-A trimming\
+      \ mode expects that sequences were both adapter and quality  before looking\
+      \ for Poly-A tails, and it is the user's responsibility to carry out an initial\
+      \ round of trimming."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--implicon"
+    description: "This is a special mode of operation for paired-end data, such as\
+      \ required for the IMPLICON method, where a UMI sequence is getting transferred\
+      \ from the start of Read 2 to the readID of both reads. Following this, Trim\
+      \ Galore will exit. In it's current implementation, the UMI carrying reads come\
+      \ in the following format\n  Read 1  5' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\
+      \ 3'\n  Read 2  3' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5'\nWhere UUUUUUUU is\
+      \ a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual\
+      \ fragment to be sequenced. The UMI of Read 2 (R2) is written into the read\
+      \ ID of both reads and removed from the actual sequence.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "RRBS-specific options"
+  arguments:
+  - type: "boolean"
+    name: "--rrbs"
+    description: "Specifies that the input file was an MspI digested RRBS sample (recognition\
+      \ site is CCGG). Single-end or Read 1 sequences (paired-end) which were adapter-trimmed\
+      \ will have a further 2 bp removed from their 3' end. Sequences which were merely\
+      \ trimmed because of poor quality will not be shortened further. Read 2 of paired-end\
+      \ libraries will in addition have the first 2 bp removed from the 5' end (by\
+      \ setting '--clip_r2 2'). This is to avoid using artificial methylation calls\
+      \ from the filled-in cytosine positions close to the 3' MspI site in sequenced\
+      \ fragments. This option is not recommended for users of the Tecan Ovation RRBS\
+      \ Methyl-Seq with TrueMethyl oxBS 1-16 kit (see below)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--non_directional"
+    description: "Selecting this option for non-directional RRBS libraries will screen\
+      \ quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and,\
+      \ if found, removes the first two basepairs. Like with the option '--rrbs' this\
+      \ avoids using cytosine positions that were filled-in during the end-repair\
+      \ step. '--non_directional' requires '--rrbs' to be specified as well. Note\
+      \ that this option does not set '--clip_r2 2' in paired-end mode."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--keep"
+    description: "Keep the quality trimmed intermediate file."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Paired-end specific options"
+  arguments:
+  - type: "boolean"
+    name: "--paired"
+    description: "This option performs length trimming of quality/adapter/RRBS trimmed\
+      \ reads for paired-end files. To pass the validation test, both sequences of\
+      \ a sequence pair are required to have a certain minimum length which is governed\
+      \ by the option --length (see above). If only one read passes this length threshold\
+      \ the other read can be rescued (see option --retain_unpaired). Using this option\
+      \ lets you discard too short read pairs without disturbing the sequence-by-sequence\
+      \ order of FastQ files which is required by many aligners. Trim Galore expects\
+      \ paired-end files to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq\
+      \ SRR2_1.fq.gz SRR2_2.fq.gz ... ."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--retain_unpaired"
+    description: "If only one of the two paired-end reads became too short, the longer\
+      \ read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output\
+      \ files. The length cutoff for unpaired single-end reads is governed by the\
+      \ parameters -r1/--length_1 and -r2/--length_2."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--length_1"
+    alternatives:
+    - "-r1"
+    description: "Unpaired single-end read length cutoff needed for read 1 to be written\
+      \ to '.unpaired_1.fq' output file. These reads may be mapped in single-end mode."
+    info: null
+    example:
+    - 35
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--length_2"
+    alternatives:
+    - "-r2"
+    description: "Unpaired single-end read length cutoff needed for read 2 to be written\
+      \ to '.unpaired_2.fq' output file. These reads may be mapped in single-end mode."
+    info: null
+    example:
+    - 35
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_dir"
+    alternatives:
+    - "-o"
+    description: "If specified all output will be written to this directory instead\
+      \ of the current directory."
+    info: null
+    default:
+    - "trimmed_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_r1"
+    description: "Output file for read 1. Only works when 1 file (single-end) or 2\
+      \ files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "read_1.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_r2"
+    description: "Output file for read 2. Only works when 1 file (single-end) or 2\
+      \ files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "read_2.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimming_report_r1"
+    description: "Trimming report for read 1. Only works when 1 file (single-end)\
+      \ or 2 files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "read_1.trimming_report.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimming_report_r2"
+    description: "Trimming report for read 1. Only works when 1 file (single-end)\
+      \ or 2 files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "read_2.trimming_report.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_fastqc_html_1"
+    description: "FastQC report for trimmed (single-end) reads (or read 1 for paired-end).\
+      \ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
+      \ but not for longer lists."
+    info: null
+    example:
+    - "read_1.fastqc.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_fastqc_html_2"
+    description: "FastQC report for trimmed reads (read2 for paired-end). Only works\
+      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
+      \ longer lists."
+    info: null
+    example:
+    - "read_2.fastqc.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_fastqc_zip_1"
+    description: "FastQC results for trimmed (single-end) reads (or read 1 for paired-end).\
+      \ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
+      \ but not for longer lists."
+    info: null
+    example:
+    - "read_1.fastqc.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trimmed_fastqc_zip_2"
+    description: "FastQC results for trimmed reads (read2 for paired-end). Only works\
+      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
+      \ longer lists."
+    info: null
+    example:
+    - "read_2.fastqc.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--unpaired_r1"
+    description: "Output file for unpired read 1. Only works when 1 file (single-end)\
+      \ or 2 files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "unpaired_read_1.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--unpaired_r2"
+    description: "Output file for unpaired read 2. Only works when 1 file (single-end)\
+      \ or 2 files (paired-end) are specified, but not for longer lists."
+    info: null
+    example:
+    - "unpaired_read_2.fastq"
+    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: "A wrapper tool around Cutadapt and FastQC to consistently apply quality\
+  \ and adapter trimming to FastQ files. \n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "trimming"
+- "adapters"
+license: "GPL-3.0"
+links:
+  repository: "https://github.com/FelixKrueger/TrimGalore"
+  homepage: "https://github.com/FelixKrueger/TrimGalore"
+  documentation: "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md"
+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/trim-galore:0.6.9--hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo \"TrimGalore: `trim_galore --version | sed -n 's/.*version\\s\\+\\([0-9]\\\
+      +\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p'`\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/trimgalore/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/trimgalore"
+  executable: "target/executable/trimgalore/trimgalore"
+  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"

target/executable/tx2gene/.config.vsh.yaml

@@ -0,0 +1,203 @@
+name: "tx2gene"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--quant_results"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--gtf"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_extra_attributes"
+    info: null
+    default:
+    - "gene_name"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_group_features"
+    info: null
+    default:
+    - "gene_id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quant_type"
+    description: "Method used for quantification"
+    info: null
+    required: false
+    choices:
+    - "salmon"
+    - "kallisto"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--tsv"
+    info: null
+    default:
+    - "tx2gene.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--updated_versions"
+    info: null
+    default:
+    - "versions.yml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "tx2gene.py"
+description: "Get transcript id (tx) to gene names for tximport"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/tx2gene/main.nf"
+    last_sha: "839ac5cab892504514cc96d44e99e70516b239d2"
+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: "apt"
+    packages:
+    - "pip"
+    - "unzip"
+    interactive: false
+  - type: "python"
+    user: false
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/tx2gene/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/tx2gene"
+  executable: "target/executable/tx2gene/tx2gene"
+  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"

target/executable/tx2gene/tx2gene.py

@@ -0,0 +1,169 @@
+
+#!/usr/bin/env python
+
+# Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license.
+
+import logging
+import argparse
+import glob
+import os
+import re
+from collections import Counter, defaultdict, OrderedDict
+from collections.abc import Set
+from typing import Dict
+
+# Configure logging
+logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]:
+    """
+    Read the top 100 transcripts from the quantification file.
+
+    Parameters:
+    quant_dir (str): Directory where quantification files are located.
+    file_pattern (str): Pattern to match quantification files.
+
+    Returns:
+    set: A set containing the top 100 transcripts.
+    """
+    try:
+        # Find the quantification file within the directory
+        quant_file_path = glob.glob(os.path.join(quant_dir, file_pattern))[0]
+        with open(quant_file_path, "r") as file_handle:
+            # Read the file and extract the top 100 transcripts
+            return {line.split()[0] for i, line in enumerate(file_handle) if i > 0 and i <= 100}
+    except IndexError:
+        # Log an error and raise a FileNotFoundError if the quant file does not exist
+        logger.error("No quantification files found.")
+        raise FileNotFoundError("Quantification file not found.")
+
+
+def discover_transcript_attribute(gtf_file: str, transcripts: Set[str]) -> str:
+    """
+    Discover the attribute in the GTF that corresponds to transcripts, prioritizing 'transcript_id'.
+
+    Parameters:
+    gtf_file (str): Path to the GTF file.
+    transcripts (Set[str]): A set of transcripts to match in the GTF file.
+
+    Returns:
+    str: The attribute name that corresponds to transcripts in the GTF file.
+    """
+
+    votes = Counter()
+    with open(gtf_file) as inh:
+        # Read GTF file, skipping header lines
+        for line in filter(lambda x: not x.startswith("#"), inh):
+            cols = line.split("\t")
+
+            # Use regular expression to correctly split the attributes string
+            attributes_str = cols[8]
+            attributes = dict(re.findall(r'(\S+) "(.*?)(?<!\\)";', attributes_str))
+
+            votes.update(key for key, value in attributes.items() if value in transcripts)
+
+    if not votes:
+        # Log a warning if no matching attribute is found
+        logger.warning("No attribute in GTF matching transcripts")
+        return ""
+
+    # Check if 'transcript_id' is among the attributes with the highest votes
+    if "transcript_id" in votes and votes["transcript_id"] == max(votes.values()):
+        logger.info("Attribute 'transcript_id' corresponds to transcripts.")
+        return "transcript_id"
+
+    # If 'transcript_id' isn't the highest, determine the most common attribute that matches the transcripts
+    attribute, _ = votes.most_common(1)[0]
+    logger.info(f"Attribute '{attribute}' corresponds to transcripts.")
+    return attribute
+
+
+def parse_attributes(attributes_text: str) -> Dict[str, str]:
+    """
+    Parse the attributes column of a GTF file.
+
+    :param attributes_text: The attributes column as a string.
+    :return: A dictionary of the attributes.
+    """
+    # Split the attributes string by semicolon and strip whitespace
+    attributes = attributes_text.strip().split(";")
+    attr_dict = OrderedDict()
+
+    # Iterate over each attribute pair
+    for attribute in attributes:
+        # Split the attribute into key and value, ensuring there are two parts
+        parts = attribute.strip().split(" ", 1)
+        if len(parts) == 2:
+            key, value = parts
+            # Remove any double quotes from the value
+            value = value.replace('"', "")
+            attr_dict[key] = value
+
+    return attr_dict
+
+
+def map_transcripts_to_gene(
+    quant_type: str, gtf_file: str, quant_dir: str, gene_id: str, extra_id_field: str, output_file: str
+) -> bool:
+    """
+    Map transcripts to gene names and write the output to a file.
+
+    Parameters:
+    quant_type (str): The quantification method used (e.g., 'salmon').
+    gtf_file (str): Path to the GTF file.
+    quant_dir (str): Directory where quantification files are located.
+    gene_id (str): The gene ID attribute in the GTF file.
+    extra_id_field (str): Additional ID field in the GTF file.
+    output_file (str): The output file path.
+
+    Returns:
+    bool: True if the operation was successful, False otherwise.
+    """
+    # Read the top transcripts based on quantification type
+    transcripts = read_top_transcripts(quant_dir, "*quant_results.sf" if quant_type == "salmon" else "*abundance.tsv")
+    # Discover the attribute that corresponds to transcripts in the GTF
+    transcript_attribute = discover_transcript_attribute(gtf_file, transcripts)
+
+    if not transcript_attribute:
+        # If no attribute is found, return False
+        return False
+
+    # Open GTF and output file to write the mappings
+    # Initialize the set to track seen combinations
+    seen = set()
+
+    with open(gtf_file) as inh, open(output_file, "w") as output_handle:
+        # Parse each line of the GTF, mapping transcripts to genes
+        for line in filter(lambda x: not x.startswith("#"), inh):
+            cols = line.split("\t")
+            attr_dict = parse_attributes(cols[8])
+            if gene_id in attr_dict and transcript_attribute in attr_dict:
+                # Create a unique identifier for the transcript-gene combination
+                transcript_gene_pair = (attr_dict[transcript_attribute], attr_dict[gene_id])
+
+                # Check if the combination has already been seen
+                if transcript_gene_pair not in seen:
+                    # If it's a new combination, write it to the output and add to the seen set
+                    extra_id = attr_dict.get(extra_id_field, attr_dict[gene_id])
+                    output_handle.write(f"{attr_dict[transcript_attribute]}\t{attr_dict[gene_id]}\t{extra_id}\n")
+                    seen.add(transcript_gene_pair)
+
+    return True
+
+
+# Main function to parse arguments and call the mapping function
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Map transcripts to gene names for tximport.")
+    parser.add_argument("--quant_type", type=str, help="Quantification type", default="salmon")
+    parser.add_argument("--gtf", type=str, help="GTF file", required=True)
+    parser.add_argument("--quants", type=str, help="Output of quantification", required=True)
+    parser.add_argument("--id", type=str, help="Gene ID in the GTF file", required=True)
+    parser.add_argument("--extra", type=str, help="Extra ID in the GTF file")
+    parser.add_argument("-o", "--output", dest="output", default="tx2gene.tsv", type=str, help="File with output")
+
+    args = parser.parse_args()
+    if not map_transcripts_to_gene(args.quant_type, args.gtf, args.quants, args.id, args.extra, args.output):
+        logger.error("Failed to map transcripts to genes.")

target/executable/tximport/.config.vsh.yaml

@@ -0,0 +1,258 @@
+name: "tximport"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--quant_results"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--tx2gene_tsv"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quant_type"
+    description: "Method used for quantification"
+    info: null
+    required: false
+    choices:
+    - "salmon"
+    - "kallisto"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--tpm_gene"
+    info: null
+    default:
+    - "merged.gene_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene"
+    info: null
+    default:
+    - "merged.gene_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_length_scaled"
+    info: null
+    default:
+    - "merged.gene_counts_length_scaled.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_scaled"
+    info: null
+    default:
+    - "merged.gene_counts_scaled.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--lengths_gene"
+    info: null
+    default:
+    - "merged.gene_length.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tpm_transcript"
+    info: null
+    default:
+    - "merged.transcript_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_transcript"
+    info: null
+    default:
+    - "merged.transcript_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--lengths_transcript"
+    info: null
+    default:
+    - "merged.transcript_length.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "tximport.r"
+description: "Get dataframe linking transcript ID, gene ID, and gene name"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/tximport/main.nf"
+    last_sha: "489bcb4efdc7bd58839b22b0360d26b4d80b87a8"
+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: "apt"
+    packages:
+    - "r-base"
+    - "libcurl4-openssl-dev"
+    - "libssl-dev"
+    - "libxml2-dev"
+    interactive: false
+  - type: "r"
+    cran:
+    - "jsonlite"
+    bioc:
+    - "SummarizedExperiment"
+    - "tximport"
+    - "tximeta"
+    bioc_force_install: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/tximport/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/tximport"
+  executable: "target/executable/tximport/tximport"
+  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"

target/executable/tximport/tximport.r

@@ -0,0 +1,141 @@
+#!/usr/bin/env Rscript
+
+# Script for importing and processing transcript-level quantifications.
+# Written by Lorena Pantano, later modified by Jonathan Manning, and released under the MIT license.
+
+# Loading required libraries
+library(SummarizedExperiment)
+library(tximport)
+
+# Parsing command line arguments
+args <- commandArgs(trailingOnly=TRUE)
+if (length(args) < 4) {
+    stop("Usage: tximport.r <coldata_path> <path> <prefix> <quant_type> <tx2gene_path>",
+        call.=FALSE)
+}
+
+# Assigning command line arguments to variables
+coldata_path <- args[1]
+path <- args[2]
+prefix <- args[3]
+quant_type <- args[4]
+tx2gene_path <- args[5]
+
+## Functions
+
+# Build a table from a SummarizedExperiment object
+build_table <- function(se.obj, slot) {
+    cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]])
+}
+
+# Write a table to a file with given parameters
+write_se_table <- function(params) {
+    file_name <- paste0(prefix, ".", params$suffix)
+    write.table(build_table(params$obj, params$slot), file_name,
+                sep="\t", quote=FALSE, row.names = FALSE)
+}
+
+# Read transcript metadata from a given path
+read_transcript_info <- function(tinfo_path){
+    info <- file.info(tinfo_path)
+    if (info$size == 0) {
+        stop("tx2gene file is empty")
+    }
+
+    transcript_info <- read.csv(tinfo_path, sep="\t", header = FALSE,
+                                col.names = c("tx", "gene_id", "gene_name"))
+
+    extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]]))
+    transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra))
+    transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ]
+    rownames(transcript_info) <- transcript_info[["tx"]]
+
+    list(transcript = transcript_info,
+        gene = unique(transcript_info[,2:3]),
+        tx2gene = transcript_info[,1:2])
+}
+
+# Read and process sample/column data from a given path
+read_coldata <- function(coldata_path){
+    if (file.exists(coldata_path)) {
+        coldata <- read.csv(coldata_path, sep="\t")
+        coldata <- coldata[match(names, coldata[,1]),]
+        coldata <- cbind(files = fns, coldata)
+    } else {
+        message("ColData not available: ", coldata_path)
+        coldata <- data.frame(files = fns, names = names)
+    }
+    rownames(coldata) <- coldata[["names"]]
+}
+
+# Create a SummarizedExperiment object with given data
+create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) {
+    SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length),
+        colData = col_data,
+        rowData = row_data)
+}
+
+# Main script starts here
+
+# Define pattern for file names based on quantification type
+pattern <- ifelse(quant_type == "kallisto", "abundance.tsv", ".*quant_results\\.sf")
+fns <- list.files(path, pattern = pattern, recursive = T, full.names = T)
+names <- basename(fns)
+names(fns) <- names
+dropInfReps <- quant_type == "kallisto"
+
+# Import transcript-level quantifications
+txi <- tximport(fns, type = quant_type, txOut = TRUE, dropInfReps = dropInfReps)
+
+# Read transcript and sample data
+transcript_info <- read_transcript_info(tx2gene_path)
+coldata <- read_coldata(coldata_path)
+
+# Create initial SummarizedExperiment object
+se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]],
+    DataFrame(coldata), transcript_info$transcript)
+
+# Setting parameters for writing tables
+params <- list(
+    list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"),
+    list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"),
+    list(obj = se, slot = "length", suffix = "transcript_lengths.tsv")
+)
+
+# Process gene-level data if tx2gene mapping is available
+if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info$tx2gene)) {
+    tx2gene <- transcript_info$tx2gene
+    gi <- summarizeToGene(txi, tx2gene = tx2gene)
+    gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM")
+    gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM")
+
+    gene_info <- transcript_info$gene[match(rownames(gi[[1]]), transcript_info$gene[["gene_id"]]),]
+    rownames(gene_info) <- gene_info[["tx"]]
+
+    col_data_frame <- DataFrame(coldata)
+
+    # Create gene-level SummarizedExperiment objects
+    gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]],
+        col_data_frame, gene_info)
+    gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]],
+        col_data_frame, gene_info)
+    gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]],
+        col_data_frame, gene_info)
+
+    params <- c(params, list(
+        list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"),
+        list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"),
+        list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"),
+        list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"),
+        list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"),
+        list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"),
+        list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv")
+    ))
+}
+
+# Writing tables for each set of parameters
+done <- lapply(params, write_se_table)
+
+# Output session information and citations
+citation("tximeta")
+sessionInfo()

target/executable/ucsc/bedclip/.config.vsh.yaml

@@ -0,0 +1,175 @@
+name: "bedclip"
+namespace: "ucsc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input_bedgraph"
+    description: "bedGraph file which should be converted"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sizes"
+    description: "File with chromosome sizes"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_bedgraph"
+    description: "bedGraph file after clipping"
+    info: null
+    default:
+    - "$id.$key.bedgraph"
+    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: "Remove lines from bed file that refer to off-chromosome locations"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.bedgraph"
+- type: "file"
+  path: "genome.sizes"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/ucsc/bedclip/main.nf"
+    - "modules/nf-core/ucsc/bedclip/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "rsync"
+    - "libcurl4"
+    interactive: false
+  - type: "docker"
+    run:
+    - "rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/ucsc/bedclip/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/ucsc/bedclip"
+  executable: "target/executable/ucsc/bedclip/bedclip"
+  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"

target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml

@@ -0,0 +1,175 @@
+name: "bedgraphtobigwig"
+namespace: "ucsc"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bedgraph"
+    description: "bedGraph file which should be converted"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sizes"
+    description: "File with chromosome sizes"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--bigwig"
+    description: "bigWig coverage file relative to genes on the input file"
+    info: null
+    default:
+    - "$id.$key.bigwig"
+    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: "Convert a bedGraph file to bigWig format"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test.bedgraph"
+- type: "file"
+  path: "genome.sizes"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/ucsc/bedgraphtobigwig/main.nf"
+    - "modules/nf-core/ucsc/bedgraphtobigwig/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "rsync"
+    - "libcurl4"
+    interactive: false
+  - type: "docker"
+    run:
+    - "rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/ucsc/bedgraphtobigwig/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/ucsc/bedgraphtobigwig"
+  executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
+  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"

target/executable/umitools/umitools_dedup/.config.vsh.yaml

@@ -0,0 +1,206 @@
+name: "umitools_dedup"
+namespace: "umitools"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - 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: "--bai"
+    description: "BAM index"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--get_output_stats"
+    description: "Whether or not to generate output stats."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_bam"
+    description: "Deduplicated BAM file"
+    info: null
+    default:
+    - "$id.$key.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_stats"
+    description: "Directory containing UMI based dedupllication statistics files"
+    info: null
+    default:
+    - "$id.umi_dedup.stats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Deduplicate reads based on the mapping co-ordinate and the UMI attached\
+  \ to the read.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "chr19.bam"
+- type: "file"
+  path: "chr19.bam.bai"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/umitools/dedup/main.nf"
+    - "modules/nf-core/umitools/dedup/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "umi_tools"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/umitools/umitools_dedup/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/umitools/umitools_dedup"
+  executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
+  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"

target/executable/umitools/umitools_extract/.config.vsh.yaml

@@ -0,0 +1,264 @@
+name: "umitools_extract"
+namespace: "umitools"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files, either one or two (paired)"
+    info: null
+    example:
+    - "sample.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "string"
+    name: "--bc_pattern"
+    description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
+      \ first 6 nucleotides of the read are from the UMI."
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fastq_1"
+    description: "Output file for read 1."
+    info: null
+    default:
+    - "$id.$key.read_1.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Output file for read 2."
+    info: null
+    default:
+    - "$id.$key.read_2.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Optional arguments"
+  arguments:
+  - type: "string"
+    name: "--umitools_extract_method"
+    description: "UMI pattern to use."
+    info: null
+    default:
+    - "string"
+    required: false
+    choices:
+    - "string"
+    - "regex"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_umi_separator"
+    description: "The character that separates the UMI in the read name. Most likely\
+      \ a colon if you skipped the extraction with UMI-tools and used other software."
+    info: null
+    default:
+    - "_"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_grouping_method"
+    description: "Method to use to determine read groups by subsuming those with similar\
+      \ UMIs. All methods start by identifying the reads with the same mapping position,\
+      \ but treat similar yet nonidentical UMIs differently."
+    info: null
+    default:
+    - "directional"
+    required: false
+    choices:
+    - "unique"
+    - "percentile"
+    - "cluster"
+    - "adjacency"
+    - "directional"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--umi_discard_read"
+    description: "After UMI barcode extraction discard either R1 or R2 by setting\
+      \ this parameter to 1 or 2, respectively."
+    info: null
+    default:
+    - 0
+    required: false
+    choices:
+    - 0
+    - 1
+    - 2
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "UMI-tools contains tools for dealing with Unique Molecular Identifiers\
+  \ (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See\
+  \ https://umi-tools.readthedocs.io/en/latest/ for more information.\nThis component\
+  \ flexible removes UMI sequences from fastq reads. UMIs are removed and appended\
+  \ to the read name.\nThis component extracts UMI barcode from a read and add it\
+  \ to the read name, leaving any sample barcode in place\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "scrb_seq_fastq.1.gz"
+- type: "file"
+  path: "scrb_seq_fastq.2.gz"
+- type: "file"
+  path: "slim.fastq.gz"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/nf-core/umitools/extract/main.nf"
+    - "modules/nf-core/umitools/extract/meta.yml"
+    last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
+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: "apt"
+    packages:
+    - "pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "umi_tools"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/umitools/umitools_extract/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/umitools/umitools_extract"
+  executable: "target/executable/umitools/umitools_extract/umitools_extract"
+  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"

target/executable/umitools_prepareforquant/.config.vsh.yaml

@@ -0,0 +1,167 @@
+name: "umitools_prepareforquant"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bam"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "$id.transcriptome_sorted.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--log"
+    info: null
+    default:
+    - "$id.$key.log"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "prepare-for-rsem.py"
+description: "Fix paired-end reads in name sorted BAM file to prepare for salmon quantification"
+info:
+  migration_info:
+    git_repo: "https://github.com/nf-core/rnaseq.git"
+    paths:
+    - "modules/local/umitools_prepareforrsem.nf"
+    last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "apt"
+    packages:
+    - "pip"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "umi_tools"
+    - "pysam"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/umitools_prepareforquant/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/umitools_prepareforquant"
+  executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
+  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"

target/executable/umitools_prepareforquant/prepare-for-rsem.py

@@ -0,0 +1,270 @@
+#!/usr/bin/env python3
+
+"""
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Credits
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This script is a clone of the "prepare-for-rsem.py" script written by
+Ian Sudbury, Tom Smith and other contributors to the UMI-tools package:
+https://github.com/CGATOxford/UMI-tools
+
+It has been included here to address problems encountered with
+Salmon quant and RSEM as discussed in the issue below:
+https://github.com/CGATOxford/UMI-tools/issues/465
+
+When the "umi_tools prepare-for-rsem" command becomes available in an official
+UMI-tools release this script will be replaced and deprecated.
+
+Commit:
+https://github.com/CGATOxford/UMI-tools/blob/bf8608d6a172c5ca0dcf33c126b4e23429177a72/umi_tools/prepare-for-rsem.py
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+prepare_for_rsem - make the output from dedup or group compatible with RSEM
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The SAM format specification states that the mnext and mpos fields should point
+to the primary alignment of a read's mate. However, not all aligners adhere to
+this standard. In addition, the RSEM software requires that the mate of a read1
+appears directly after it in its input BAM. This requires that there is exactly
+one read1 alignment for every read2 and vice versa.
+
+In general (except in a few edge cases) UMI tools outputs only the read2 to that
+corresponds to the read specified in the mnext and mpos positions of a selected
+read1, and only outputs this read once, even if multiple read1s point to it.
+This makes UMI-tools outputs incompatible with RSEM. This script takes the output
+from dedup or groups and ensures that each read1 has exactly one read2 (and vice
+versa), that read2 always appears directly after read1,and that pairs point to
+each other (note this is technically not valid SAM format). Copy any specified
+tags from read1 to read2 if they are present (by default, UG and BX, the unique
+group and correct UMI tags added by _group_)
+
+Input must to name sorted.
+
+
+https://raw.githubusercontent.com/CGATOxford/UMI-tools/master/LICENSE
+
+"""
+
+from umi_tools import Utilities as U
+from collections import defaultdict, Counter
+import pysam
+import sys
+
+usage = """
+prepare_for_rsem - make output from dedup or group compatible with RSEM
+
+Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
+
+       note: If --stdout is omited, standard out is output. To
+             generate a valid BAM file on standard out, please
+             redirect log with --log=LOGFILE or --log2stderr """
+
+
+def chunk_bam(bamfile):
+    """Take in a iterator of pysam.AlignmentSegment entries and yield
+    lists of reads that all share the same name"""
+
+    last_query_name = None
+    output_buffer = list()
+
+    for read in bamfile:
+        if last_query_name is not None and last_query_name != read.query_name:
+            yield (output_buffer)
+            output_buffer = list()
+
+        last_query_name = read.query_name
+        output_buffer.append(read)
+
+    yield (output_buffer)
+
+
+def copy_tags(tags, read1, read2):
+    """Given a  list of tags, copies the values of these tags from read1
+    to read2, if the tag is set"""
+
+    for tag in tags:
+        try:
+            read1_tag = read1.get_tag(tag, with_value_type=True)
+            read2.set_tag(tag, value=read1_tag[0], value_type=read1_tag[1])
+        except KeyError:
+            pass
+
+    return read2
+
+
+def pick_mate(read, template_dict, mate_key):
+    """Find the mate of read in the template dict using key. It will retrieve
+    all reads at that key, and then scan to pick the one that refers to _read_
+    as it's mate. If there is no such read, it picks a first one it comes to"""
+
+    mate = None
+
+    # get a list of secondary reads at the correct alignment position
+    potential_mates = template_dict[not read.is_read1][mate_key]
+
+    # search through one at a time to find a read that points to the current read
+    # as its mate.
+    for candidate_mate in potential_mates:
+        if (
+            candidate_mate.next_reference_name == read.reference_name
+            and candidate_mate.next_reference_start == read.pos
+        ):
+            mate = candidate_mate
+
+    # if no such read is found, then pick any old secondary alignment at that position
+    # note: this happens when UMI-tools outputs the wrong read as something's pair.
+    if mate is None and len(potential_mates) > 0:
+        mate = potential_mates[0]
+
+    return mate
+
+
+def main(argv=None):
+    if argv is None:
+        argv = sys.argv
+
+    # setup command line parser
+    parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"])
+    group = U.OptionGroup(parser, "RSEM preparation specific options")
+
+    group.add_option(
+        "--tags",
+        dest="tags",
+        type="string",
+        default="UG,BX",
+        help="Comma-separated list of tags to transfer from read1 to read2",
+    )
+    group.add_option(
+        "--sam", dest="sam", action="store_true", default=False, help="input and output SAM rather than BAM"
+    )
+
+    parser.add_option_group(group)
+
+    # add common options (-h/--help, ...) and parse command line
+    (options, args) = U.Start(
+        parser, argv=argv, add_group_dedup_options=False, add_umi_grouping_options=False, add_sam_options=False
+    )
+
+    skipped_stats = Counter()
+
+    if options.stdin != sys.stdin:
+        in_name = options.stdin.name
+        options.stdin.close()
+    else:
+        in_name = "-"
+
+    if options.sam:
+        mode = ""
+    else:
+        mode = "b"
+
+    inbam = pysam.AlignmentFile(in_name, "r" + mode)
+
+    if options.stdout != sys.stdout:
+        out_name = options.stdout.name
+        options.stdout.close()
+    else:
+        out_name = "-"
+
+    outbam = pysam.AlignmentFile(out_name, "w" + mode, template=inbam)
+
+    options.tags = options.tags.split(",")
+
+    for template in chunk_bam(inbam):
+        assert len(set(r.query_name for r in template)) == 1
+        current_template = {True: defaultdict(list), False: defaultdict(list)}
+
+        for read in template:
+            key = (read.reference_name, read.pos, not read.is_secondary)
+            current_template[read.is_read1][key].append(read)
+
+        output = set()
+
+        for read in template:
+            mate = None
+
+            # if this read is a non_primary alignment, we first want to check if it has a mate
+            # with the non-primary alignment flag set.
+
+            mate_key_primary = True
+            mate_key_secondary = (read.next_reference_name, read.next_reference_start, False)
+
+            # First look for a read that has the same primary/secondary status
+            # as read (i.e. secondary mate for secondary read, and primary mate
+            # for primary read)
+            mate_key = (read.next_reference_name, read.next_reference_start, read.is_secondary)
+            mate = pick_mate(read, current_template, mate_key)
+
+            # If none was found then look for the opposite (primary mate of secondary
+            # read or seconadary mate of primary read)
+            if mate is None:
+                mate_key = (read.next_reference_name, read.next_reference_start, not read.is_secondary)
+                mate = pick_mate(read, current_template, mate_key)
+
+            # If we still don't have a mate, then their can't be one?
+            if mate is None:
+                skipped_stats["no_mate"] += 1
+                U.warn(
+                    "Alignment {} has no mate -- skipped".format(
+                        "\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
+                    )
+                )
+                continue
+
+            # because we might want to make changes to the read, but not have those changes reflected
+            # if we need the read again,we copy the read. This is only way I can find to do this.
+            read = pysam.AlignedSegment().from_dict(read.to_dict(), read.header)
+            mate = pysam.AlignedSegment().from_dict(mate.to_dict(), read.header)
+
+            # Make it so that if our read is secondary, the mate is also secondary. We don't make the
+            # mate primary if the read is primary because we would otherwise end up with mulitple
+            # primary alignments.
+            if read.is_secondary:
+                mate.is_secondary = True
+
+            # In a situation where there is already one mate for each read, then we will come across
+            # each pair twice - once when we scan read1 and once when we scan read2. Thus we need
+            # to make sure we don't output something already output.
+            if read.is_read1:
+                mate = copy_tags(options.tags, read, mate)
+                output_key = str(read) + str(mate)
+
+                if output_key not in output:
+                    output.add(output_key)
+                    outbam.write(read)
+                    outbam.write(mate)
+                    skipped_stats["pairs_output"] += 1
+
+            elif read.is_read2:
+                read = copy_tags(options.tags, mate, read)
+                output_key = str(mate) + str(read)
+
+                if output_key not in output:
+                    output.add(output_key)
+                    outbam.write(mate)
+                    outbam.write(read)
+                    skipped_stats["pairs_output"] += 1
+
+            else:
+                skipped_stats["skipped_not_read_12"] += 1
+                U.warn(
+                    "Alignment {} is neither read1 nor read2 -- skipped".format(
+                        "\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
+                    )
+                )
+                continue
+
+    if not out_name == "-":
+        outbam.close()
+
+    U.info(
+        "Total pairs output: {}, Pairs skipped - no mates: {},"
+        " Pairs skipped - not read1 or 2: {}".format(
+            skipped_stats["pairs_output"], skipped_stats["no_mate"], skipped_stats["skipped_not_read12"]
+        )
+    )
+    U.Stop()
+
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv))

target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -0,0 +1,541 @@
+name: "genome_alignment_and_quant"
+namespace: "workflows"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "ID of the sample."
+    info: null
+    example:
+    - "foo"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_1"
+    alternatives:
+    - "-i"
+    description: "Path to the sample (or read 1 of paired end sample)."
+    info: null
+    example:
+    - "input.fastq.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Path to read 2 of the sample."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity. Must be one of unstranded, forward, or\
+      \ reverse"
+    info: null
+    required: false
+    choices:
+    - "forward"
+    - "reverse"
+    - "unstranded"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "GTF file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcript_fasta"
+    description: "Fasta file of the reference transcriptome."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_index"
+    description: "STAR index directory."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--star_ignore_sjdbgtf"
+    description: "When using pre-built STAR indices do not re-extract and use splice\
+      \ junctions from the GTF file"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--seq_platform"
+    description: "Sequencing platform."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--seq_center"
+    description: "Sequencing center."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_star_align_args"
+    description: "Extra arguments to pass to STAR alignment command in addition to\
+      \ defaults defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bam_csi_index"
+    description: "Create a CSI index for BAM files instead of the traditional BAI\
+      \ index. This will be required for genomes with larger chromosome sizes."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--umi_dedup_stats"
+    description: "Generate output stats when running \"umi_tools dedup\"."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--with_umi"
+    description: "Enable UMI-based read deduplication."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--salmon_quant_libtype"
+    description: "Override Salmon library type inferred based on strandedness defined\
+      \ in meta object."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_salmon_quant_args"
+    description: "Extra arguments to pass to salmon quant command in addition to defaults\
+      \ defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_group_features"
+    description: "Define the attribute type used to group features in the GTF file\
+      \ when running Salmon."
+    info: null
+    default:
+    - "gene_id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_extra_attributes"
+    description: "By default, the pipeline uses the gene_name field to obtain additional\
+      \ gene identifiers from the input GTF file when running Salmon."
+    info: null
+    default:
+    - "gene_name"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "extra_rsem_calculate_expression_args"
+    description: "Extra arguments to pass to rsem-calculate-expression command in\
+      \ addition to defaults defined by the pipeline."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--aligner"
+    description: "Specifies the alignment algorithm to use - available options are\
+      \ 'star_salmon', 'star_rsem' and 'hisat2'."
+    info: null
+    default:
+    - "star_salmon"
+    required: false
+    choices:
+    - "star_salmon"
+    - "star_rsem"
+    - "hisat2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rsem_index"
+    description: "Path to directory for pre-built RSEM index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--salmon_index"
+    description: "Path to directory for pre-built Salmon index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--star_multiqc"
+    info: null
+    default:
+    - "$id.star_align.log"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_sorted"
+    info: null
+    default:
+    - "$id.genome.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_index"
+    info: null
+    default:
+    - "$id.genome.bam.bai"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_stats"
+    info: null
+    default:
+    - "$id.genome.stats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_flagstat"
+    info: null
+    default:
+    - "$id.genome.flagstat"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_idxstats"
+    info: null
+    default:
+    - "$id.genome.idxstats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_bam"
+    info: null
+    default:
+    - "$id.transcriptome.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_bam_index"
+    info: null
+    default:
+    - "$id.transcriptome.bam.bai"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_bam_stats"
+    info: null
+    default:
+    - "$id.transcriptome.stats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_bam_flagstat"
+    info: null
+    default:
+    - "$id.transcriptome.flagstat"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_bam_idxstats"
+    info: null
+    default:
+    - "$id.transcriptome.idxstats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--quant_out_dir"
+    info: null
+    default:
+    - "$id.salmon_quant"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--quant_results_file"
+    info: null
+    default:
+    - "$id.quant.sf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "A viash sub-workflow for genome alignment and quantification stage of\
+  \ nf-core/rnaseq pipeline.\n"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "star/star_align_reads"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "samtools/samtools_sort"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "samtools/samtools_index"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "samtools/samtools_stats"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "samtools/samtools_flagstat"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "samtools/samtools_idxstats"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "umitools/umitools_dedup"
+  repository:
+    type: "local"
+- name: "umitools_prepareforquant"
+  repository:
+    type: "local"
+- name: "salmon/salmon_quant"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+- name: "rsem/rsem_calculate_expression"
+  repository:
+    type: "local"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/genome_alignment_and_quant/config.vsh.yaml"
+  runner: "executable"
+  engine: "native"
+  output: "target/executable/workflows/genome_alignment_and_quant"
+  executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+  dependencies:
+  - "target/dependencies/vsh/vsh/biobox/nextflow/star/star_align_reads"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_sort"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_index"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_stats"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_flagstat"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_idxstats"
+  - "target/nextflow/umitools/umitools_dedup"
+  - "target/nextflow/umitools_prepareforquant"
+  - "target/dependencies/vsh/vsh/biobox/nextflow/salmon/salmon_quant"
+  - "target/nextflow/rsem/rsem_calculate_expression"
+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"

target/executable/workflows/merge_quant_results/.config.vsh.yaml

@@ -0,0 +1,293 @@
+name: "merge_quant_results"
+namespace: "workflows"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--salmon_quant_results"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--kallisto_quant_results"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "file"
+    name: "--gtf"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_extra_attributes"
+    info: null
+    default:
+    - "gene_name"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gtf_group_features"
+    info: null
+    default:
+    - "gene_id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quant_type"
+    description: "Quantification method used."
+    info: null
+    default:
+    - "salmon"
+    required: false
+    choices:
+    - "salmon"
+    - "kallisto"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--versions"
+    info: null
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--tpm_gene"
+    info: null
+    example:
+    - "gene_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene"
+    info: null
+    example:
+    - "gene_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_length_scaled"
+    info: null
+    example:
+    - "gene_counts_length_scaled.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_gene_scaled"
+    info: null
+    example:
+    - "gene_counts_scaled.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tpm_transcript"
+    info: null
+    example:
+    - "transcript_tpm.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--lengths_gene"
+    info: null
+    example:
+    - "gene_length.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts_transcript"
+    info: null
+    example:
+    - "transcript_counts.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--lengths_transcript"
+    info: null
+    example:
+    - "transcript_length.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--quant_merged_summarizedexperiment"
+    info: null
+    example:
+    - "quant_merged_summarizedexperiment"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "A sub-workflow to merge the counts obtained from salmon quant across\
+  \ all samples."
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "tx2gene"
+  repository:
+    type: "local"
+- name: "tximport"
+  repository:
+    type: "local"
+- name: "summarizedexperiment"
+  repository:
+    type: "local"
+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: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/merge_quant_results/config.vsh.yaml"
+  runner: "executable"
+  engine: "native"
+  output: "target/executable/workflows/merge_quant_results"
+  executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+  dependencies:
+  - "target/nextflow/tx2gene"
+  - "target/nextflow/tximport"
+  - "target/nextflow/summarizedexperiment"
+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"

target/executable/workflows/merge_quant_results/merge_quant_results

@@ -0,0 +1,892 @@
+#!/usr/bin/env bash
+
+# merge_quant_results main
+# 
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
+# 
+# The component may contain files which fall under a different license. The
+# authors of this component should specify the license in the header of such
+# files, or include a separate license file detailing the licenses of all included
+# files.
+
+set -e
+
+if [ -z "$VIASH_TEMP" ]; then
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
+  VIASH_TEMP=${VIASH_TEMP:-/tmp}
+fi
+
+# define helper functions
+# ViashQuote: put quotes around non flag values
+# $1     : unquoted string
+# return : possibly quoted string
+# examples:
+#   ViashQuote --foo      # returns --foo
+#   ViashQuote bar        # returns 'bar'
+#   Viashquote --foo=bar  # returns --foo='bar'
+function ViashQuote {
+  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
+    echo "$1" | sed "s#=\(.*\)#='\1'#"
+  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
+    echo "$1"
+  else
+    echo "'$1'"
+  fi
+}
+# ViashRemoveFlags: Remove leading flag
+# $1     : string with a possible leading flag
+# return : string without possible leading flag
+# examples:
+#   ViashRemoveFlags --foo=bar  # returns bar
+function ViashRemoveFlags {
+  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
+}
+# ViashSourceDir: return the path of a bash file, following symlinks
+# usage   : ViashSourceDir ${BASH_SOURCE[0]}
+# $1      : Should always be set to ${BASH_SOURCE[0]}
+# returns : The absolute path of the bash file
+function ViashSourceDir {
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
+  done
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
+}
+# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
+# usage   : ViashFindTargetDir 'ScriptPath'
+# $1      : The location from where to start the upward search
+# returns : The absolute path of the '.build.yaml' file
+function ViashFindTargetDir {
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
+  done
+  echo $source
+}
+# see https://en.wikipedia.org/wiki/Syslog#Severity_level
+VIASH_LOGCODE_EMERGENCY=0
+VIASH_LOGCODE_ALERT=1
+VIASH_LOGCODE_CRITICAL=2
+VIASH_LOGCODE_ERROR=3
+VIASH_LOGCODE_WARNING=4
+VIASH_LOGCODE_NOTICE=5
+VIASH_LOGCODE_INFO=6
+VIASH_LOGCODE_DEBUG=7
+VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
+
+# ViashLog: Log events depending on the verbosity level
+# usage: ViashLog 1 alert Oh no something went wrong!
+# $1: required verbosity level
+# $2: display tag
+# $3+: messages to display
+# stdout: Your input, prepended by '[$2] '.
+function ViashLog {
+  local required_level="$1"
+  local display_tag="$2"
+  shift 2
+  if [ $VIASH_VERBOSITY -ge $required_level ]; then
+    >&2 echo "[$display_tag]" "$@"
+  fi
+}
+
+# ViashEmergency: log events when the system is unstable
+# usage: ViashEmergency Oh no something went wrong.
+# stdout: Your input, prepended by '[emergency] '.
+function ViashEmergency {
+  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
+}
+
+# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
+# usage: ViashAlert Oh no something went wrong.
+# stdout: Your input, prepended by '[alert] '.
+function ViashAlert {
+  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
+}
+
+# ViashCritical: log events when a critical condition occurs
+# usage: ViashCritical Oh no something went wrong.
+# stdout: Your input, prepended by '[critical] '.
+function ViashCritical {
+  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
+}
+
+# ViashError: log events when an error condition occurs
+# usage: ViashError Oh no something went wrong.
+# stdout: Your input, prepended by '[error] '.
+function ViashError {
+  ViashLog $VIASH_LOGCODE_ERROR error "$@"
+}
+
+# ViashWarning: log potentially abnormal events
+# usage: ViashWarning Something may have gone wrong.
+# stdout: Your input, prepended by '[warning] '.
+function ViashWarning {
+  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
+}
+
+# ViashNotice: log significant but normal events
+# usage: ViashNotice This just happened.
+# stdout: Your input, prepended by '[notice] '.
+function ViashNotice {
+  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
+}
+
+# ViashInfo: log normal events
+# usage: ViashInfo This just happened.
+# stdout: Your input, prepended by '[info] '.
+function ViashInfo {
+  ViashLog $VIASH_LOGCODE_INFO info "$@"
+}
+
+# ViashDebug: log all events, for debugging purposes
+# usage: ViashDebug This just happened.
+# stdout: Your input, prepended by '[debug] '.
+function ViashDebug {
+  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
+}
+
+# find source folder of this component
+VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
+
+# find the root of the built components & dependencies
+VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
+
+# define meta fields
+VIASH_META_NAME="merge_quant_results"
+VIASH_META_FUNCTIONALITY_NAME="merge_quant_results"
+VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
+VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
+VIASH_META_TEMP_DIR="$VIASH_TEMP"
+
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "merge_quant_results main"
+  echo ""
+  echo "A sub-workflow to merge the counts obtained from salmon quant across all"
+  echo "samples."
+  echo ""
+  echo "Input:"
+  echo "    --salmon_quant_results"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo ""
+  echo "    --kallisto_quant_results"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo ""
+  echo "    --gtf"
+  echo "        type: file, file must exist"
+  echo ""
+  echo "    --gtf_extra_attributes"
+  echo "        type: string"
+  echo "        default: gene_name"
+  echo ""
+  echo "    --gtf_group_features"
+  echo "        type: string"
+  echo "        default: gene_id"
+  echo ""
+  echo "    --quant_type"
+  echo "        type: string"
+  echo "        default: salmon"
+  echo "        choices: [ salmon, kallisto ]"
+  echo "        Quantification method used."
+  echo ""
+  echo "    --versions"
+  echo "        type: file"
+  echo ""
+  echo "Output:"
+  echo "    --tpm_gene"
+  echo "        type: file, output, file must exist"
+  echo "        example: gene_tpm.tsv"
+  echo ""
+  echo "    --counts_gene"
+  echo "        type: file, output, file must exist"
+  echo "        example: gene_counts.tsv"
+  echo ""
+  echo "    --counts_gene_length_scaled"
+  echo "        type: file, output, file must exist"
+  echo "        example: gene_counts_length_scaled.tsv"
+  echo ""
+  echo "    --counts_gene_scaled"
+  echo "        type: file, output, file must exist"
+  echo "        example: gene_counts_scaled.tsv"
+  echo ""
+  echo "    --tpm_transcript"
+  echo "        type: file, output, file must exist"
+  echo "        example: transcript_tpm.tsv"
+  echo ""
+  echo "    --lengths_gene"
+  echo "        type: file, output, file must exist"
+  echo "        example: gene_length.tsv"
+  echo ""
+  echo "    --counts_transcript"
+  echo "        type: file, output, file must exist"
+  echo "        example: transcript_counts.tsv"
+  echo ""
+  echo "    --lengths_transcript"
+  echo "        type: file, output, file must exist"
+  echo "        example: transcript_length.tsv"
+  echo ""
+  echo "    --quant_merged_summarizedexperiment"
+  echo "        type: file, output, file must exist"
+  echo "        example: quant_merged_summarizedexperiment"
+}
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='native'
+
+# initialise array
+VIASH_POSITIONAL_ARGS=''
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        -h|--help)
+            ViashHelp
+            exit
+            ;;
+        ---v|---verbose)
+            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
+            shift 1
+            ;;
+        ---verbosity)
+            VIASH_VERBOSITY="$2"
+            shift 2
+            ;;
+        ---verbosity=*)
+            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        --version)
+            echo "merge_quant_results main"
+            exit
+            ;;
+        --salmon_quant_results)
+            if [ -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ]; then
+              VIASH_PAR_SALMON_QUANT_RESULTS="$2"
+            else
+              VIASH_PAR_SALMON_QUANT_RESULTS="$VIASH_PAR_SALMON_QUANT_RESULTS,""$2"
+            fi
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_results. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --salmon_quant_results=*)
+            if [ -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ]; then
+              VIASH_PAR_SALMON_QUANT_RESULTS=$(ViashRemoveFlags "$1")
+            else
+              VIASH_PAR_SALMON_QUANT_RESULTS="$VIASH_PAR_SALMON_QUANT_RESULTS,"$(ViashRemoveFlags "$1")
+            fi
+            shift 1
+            ;;
+        --kallisto_quant_results)
+            if [ -z "$VIASH_PAR_KALLISTO_QUANT_RESULTS" ]; then
+              VIASH_PAR_KALLISTO_QUANT_RESULTS="$2"
+            else
+              VIASH_PAR_KALLISTO_QUANT_RESULTS="$VIASH_PAR_KALLISTO_QUANT_RESULTS,""$2"
+            fi
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_results. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --kallisto_quant_results=*)
+            if [ -z "$VIASH_PAR_KALLISTO_QUANT_RESULTS" ]; then
+              VIASH_PAR_KALLISTO_QUANT_RESULTS=$(ViashRemoveFlags "$1")
+            else
+              VIASH_PAR_KALLISTO_QUANT_RESULTS="$VIASH_PAR_KALLISTO_QUANT_RESULTS,"$(ViashRemoveFlags "$1")
+            fi
+            shift 1
+            ;;
+        --gtf)
+            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --gtf=*)
+            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --gtf_extra_attributes)
+            [ -n "$VIASH_PAR_GTF_EXTRA_ATTRIBUTES" ] && ViashError Bad arguments for option \'--gtf_extra_attributes\': \'$VIASH_PAR_GTF_EXTRA_ATTRIBUTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF_EXTRA_ATTRIBUTES="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf_extra_attributes. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --gtf_extra_attributes=*)
+            [ -n "$VIASH_PAR_GTF_EXTRA_ATTRIBUTES" ] && ViashError Bad arguments for option \'--gtf_extra_attributes=*\': \'$VIASH_PAR_GTF_EXTRA_ATTRIBUTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF_EXTRA_ATTRIBUTES=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --gtf_group_features)
+            [ -n "$VIASH_PAR_GTF_GROUP_FEATURES" ] && ViashError Bad arguments for option \'--gtf_group_features\': \'$VIASH_PAR_GTF_GROUP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF_GROUP_FEATURES="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf_group_features. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --gtf_group_features=*)
+            [ -n "$VIASH_PAR_GTF_GROUP_FEATURES" ] && ViashError Bad arguments for option \'--gtf_group_features=*\': \'$VIASH_PAR_GTF_GROUP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF_GROUP_FEATURES=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --quant_type)
+            [ -n "$VIASH_PAR_QUANT_TYPE" ] && ViashError Bad arguments for option \'--quant_type\': \'$VIASH_PAR_QUANT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUANT_TYPE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_type. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --quant_type=*)
+            [ -n "$VIASH_PAR_QUANT_TYPE" ] && ViashError Bad arguments for option \'--quant_type=*\': \'$VIASH_PAR_QUANT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUANT_TYPE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --versions)
+            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_VERSIONS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --versions=*)
+            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --tpm_gene)
+            [ -n "$VIASH_PAR_TPM_GENE" ] && ViashError Bad arguments for option \'--tpm_gene\': \'$VIASH_PAR_TPM_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TPM_GENE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tpm_gene. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --tpm_gene=*)
+            [ -n "$VIASH_PAR_TPM_GENE" ] && ViashError Bad arguments for option \'--tpm_gene=*\': \'$VIASH_PAR_TPM_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TPM_GENE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --counts_gene)
+            [ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --counts_gene=*)
+            [ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene=*\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --counts_gene_length_scaled)
+            [ -n "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_length_scaled\': \'$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE_LENGTH_SCALED="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene_length_scaled. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --counts_gene_length_scaled=*)
+            [ -n "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_length_scaled=*\': \'$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE_LENGTH_SCALED=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --counts_gene_scaled)
+            [ -n "$VIASH_PAR_COUNTS_GENE_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_scaled\': \'$VIASH_PAR_COUNTS_GENE_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE_SCALED="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene_scaled. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --counts_gene_scaled=*)
+            [ -n "$VIASH_PAR_COUNTS_GENE_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_scaled=*\': \'$VIASH_PAR_COUNTS_GENE_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_GENE_SCALED=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --tpm_transcript)
+            [ -n "$VIASH_PAR_TPM_TRANSCRIPT" ] && ViashError Bad arguments for option \'--tpm_transcript\': \'$VIASH_PAR_TPM_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TPM_TRANSCRIPT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tpm_transcript. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --tpm_transcript=*)
+            [ -n "$VIASH_PAR_TPM_TRANSCRIPT" ] && ViashError Bad arguments for option \'--tpm_transcript=*\': \'$VIASH_PAR_TPM_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TPM_TRANSCRIPT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --lengths_gene)
+            [ -n "$VIASH_PAR_LENGTHS_GENE" ] && ViashError Bad arguments for option \'--lengths_gene\': \'$VIASH_PAR_LENGTHS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_LENGTHS_GENE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lengths_gene. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --lengths_gene=*)
+            [ -n "$VIASH_PAR_LENGTHS_GENE" ] && ViashError Bad arguments for option \'--lengths_gene=*\': \'$VIASH_PAR_LENGTHS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_LENGTHS_GENE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --counts_transcript)
+            [ -n "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--counts_transcript\': \'$VIASH_PAR_COUNTS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_TRANSCRIPT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_transcript. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --counts_transcript=*)
+            [ -n "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--counts_transcript=*\': \'$VIASH_PAR_COUNTS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS_TRANSCRIPT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --lengths_transcript)
+            [ -n "$VIASH_PAR_LENGTHS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--lengths_transcript\': \'$VIASH_PAR_LENGTHS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_LENGTHS_TRANSCRIPT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lengths_transcript. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --lengths_transcript=*)
+            [ -n "$VIASH_PAR_LENGTHS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--lengths_transcript=*\': \'$VIASH_PAR_LENGTHS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_LENGTHS_TRANSCRIPT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --quant_merged_summarizedexperiment)
+            [ -n "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT" ] && ViashError Bad arguments for option \'--quant_merged_summarizedexperiment\': \'$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_merged_summarizedexperiment. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --quant_merged_summarizedexperiment=*)
+            [ -n "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT" ] && ViashError Bad arguments for option \'--quant_merged_summarizedexperiment=*\': \'$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        ---engine)
+            VIASH_ENGINE_ID="$2"
+            shift 2
+            ;;
+        ---engine=*)
+            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        ---cpus)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---cpus=*)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        ---memory)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---memory=*)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        *)  # positional arg or unknown option
+            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
+            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
+            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
+            shift # past argument
+            ;;
+    esac
+done
+
+# parse positional parameters
+eval set -- $VIASH_POSITIONAL_ARGS
+
+
+if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  VIASH_ENGINE_TYPE='native'
+else
+  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: native."
+  exit 1
+fi
+
+# setting computational defaults
+
+# helper function for parsing memory strings
+function ViashMemoryAsBytes {
+  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
+  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
+  if [[ $memory =~ $memory_regex ]]; then
+    local number=${memory/[^0-9]*/}
+    local symbol=${memory/*[0-9]/}
+    
+    case $symbol in
+      b)      memory_b=$number ;;
+      kb|k)   memory_b=$(( $number * 1000 )) ;;
+      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
+      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
+      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
+      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
+      kib|ki)   memory_b=$(( $number * 1024 )) ;;
+      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
+      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
+      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
+      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
+    esac
+    echo "$memory_b"
+  fi
+}
+# compute memory in different units
+if [ ! -z ${VIASH_META_MEMORY+x} ]; then
+  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
+  # do not define other variables if memory_b is an empty string
+  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
+    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
+    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
+    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
+    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
+    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
+    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
+    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
+    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
+    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
+    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
+  else
+    # unset memory if string is empty
+    unset $VIASH_META_MEMORY_B
+  fi
+fi
+# unset nproc if string is empty
+if [ -z "$VIASH_META_CPUS" ]; then
+  unset $VIASH_META_CPUS
+fi
+
+
+# check whether required parameters exist
+if [ -z ${VIASH_META_NAME+x} ]; then
+  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
+  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
+  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
+  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_CONFIG+x} ]; then
+  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
+  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+
+# filling in defaults
+if [ -z ${VIASH_PAR_GTF_EXTRA_ATTRIBUTES+x} ]; then
+  VIASH_PAR_GTF_EXTRA_ATTRIBUTES="gene_name"
+fi
+if [ -z ${VIASH_PAR_GTF_GROUP_FEATURES+x} ]; then
+  VIASH_PAR_GTF_GROUP_FEATURES="gene_id"
+fi
+if [ -z ${VIASH_PAR_QUANT_TYPE+x} ]; then
+  VIASH_PAR_QUANT_TYPE="salmon"
+fi
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ]; then
+  IFS=','
+  set -f
+  for file in $VIASH_PAR_SALMON_QUANT_RESULTS; do
+    unset IFS
+    if [ ! -e "$file" ]; then
+      ViashError "Input file '$file' does not exist."
+      exit 1
+    fi
+  done
+  set +f
+fi
+if [ ! -z "$VIASH_PAR_KALLISTO_QUANT_RESULTS" ]; then
+  IFS=','
+  set -f
+  for file in $VIASH_PAR_KALLISTO_QUANT_RESULTS; do
+    unset IFS
+    if [ ! -e "$file" ]; then
+      ViashError "Input file '$file' does not exist."
+      exit 1
+    fi
+  done
+  set +f
+fi
+if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
+  ViashError "Input file '$VIASH_PAR_GTF' does not exist."
+  exit 1
+fi
+
+# check whether parameters values are of the right type
+if [[ -n "$VIASH_META_CPUS" ]]; then
+  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_B" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+
+# check whether value is belongs to a set of choices
+if [ ! -z "$VIASH_PAR_QUANT_TYPE" ]; then
+  VIASH_PAR_QUANT_TYPE_CHOICES=("salmon;kallisto")
+  IFS=';'
+  set -f
+  if ! [[ ";${VIASH_PAR_QUANT_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_QUANT_TYPE;" ]]; then
+    ViashError '--quant_type' specified value of \'$VIASH_PAR_QUANT_TYPE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  set +f
+  unset IFS
+fi
+
+# create parent directories of output files, if so desired
+if [ ! -z "$VIASH_PAR_TPM_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_TPM_GENE")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_TPM_GENE")"
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE")"
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED")"
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE_SCALED" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE_SCALED")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE_SCALED")"
+fi
+if [ ! -z "$VIASH_PAR_TPM_TRANSCRIPT" ] && [ ! -d "$(dirname "$VIASH_PAR_TPM_TRANSCRIPT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_TPM_TRANSCRIPT")"
+fi
+if [ ! -z "$VIASH_PAR_LENGTHS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_LENGTHS_GENE")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_LENGTHS_GENE")"
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPT")"
+fi
+if [ ! -z "$VIASH_PAR_LENGTHS_TRANSCRIPT" ] && [ ! -d "$(dirname "$VIASH_PAR_LENGTHS_TRANSCRIPT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_LENGTHS_TRANSCRIPT")"
+fi
+if [ ! -z "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT")"
+fi
+
+if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  if [ "$VIASH_MODE" == "run" ]; then
+    VIASH_CMD="bash"
+  else
+    ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
+    exit 1
+  fi
+fi
+
+
+# set dependency paths
+VIASH_DEP_TX2GENE="$VIASH_META_RESOURCES_DIR/../../../nextflow/tx2gene/main.nf"
+VIASH_DEP_TXIMPORT="$VIASH_META_RESOURCES_DIR/../../../nextflow/tximport/main.nf"
+VIASH_DEP_SUMMARIZEDEXPERIMENT="$VIASH_META_RESOURCES_DIR/../../../nextflow/summarizedexperiment/main.nf"
+
+ViashDebug "Running command: $(echo $VIASH_CMD)"
+cat << VIASHEOF | eval $VIASH_CMD
+set -e
+tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-merge_quant_results-XXXXXX").nf
+function clean_up {
+  rm "\$tempscript"
+}
+function interrupt {
+  echo -e "\nCTRL-C Pressed..."
+  exit 1
+}
+trap clean_up EXIT
+trap interrupt INT SIGINT
+cat > "\$tempscript" << 'VIASHMAIN'
+//// VIASH START
+// The following code has been auto-generated by Viash.
+
+//// VIASH END
+workflow run_wf {
+    take: 
+        input_ch
+
+    main: 
+        output_ch = input_ch
+
+        | map { id, state -> 
+            def quant_results = state.quant_type == 'kallisto' ? state.kallisto_quant_results : state.salmon_quant_results
+            [id, state + [quant_results: quant_results]]
+        }
+        
+        | tx2gene.run (
+            fromState: [ 
+                "quant_results": "quant_results", 
+                "gtf_extra_attributes": "gtf_extra_attributes", 
+                "gtf": "gtf", 
+                "gtf_group_features": "gtf_group_features", 
+                "quant_type": "quant_type"
+            ],
+            toState: [ "tx2gene_tsv": "tsv" ]
+        )
+
+        | tximport.run (
+            fromState: [ 
+                "quant_results": "quant_results", 
+                "tx2gene_tsv": "tx2gene_tsv", 
+                "quant_type": "quant_type"
+            ],
+            toState:  [
+                "tpm_gene": "tpm_gene",
+                "counts_gene": "counts_gene",
+                "counts_gene_length_scaled": "counts_gene_length_scaled",
+                "counts_gene_scaled": "counts_gene_scaled", 
+                "tpm_transcript": "tpm_transcript", 
+                "counts_transcript": "counts_transcript", 
+                "length_gene": "length_gene",
+                "length_transcript": "length_transcript"
+            ]
+        )
+        
+        | summarizedexperiment.run (
+            fromState: [ 
+                "tpm_gene": "tpm_gene",
+                "counts_gene": "counts_gene",
+                "counts_gene_length_scaled": "counts_gene_length_scaled",
+                "counts_gene_scaled": "counts_gene_scaled", 
+                "tpm_transcript": "tpm_transcript", 
+                "counts_transcript": "counts_transcript", 
+                "tx2gene_tsv": "tx2gene_tsv"
+            ],
+            toState: [ "quant_merged_summarizedexperiment": "output" ]
+        )
+
+        | setState (
+            [ "tpm_gene": "tpm_gene",
+            "counts_gene": "counts_gene",
+            "counts_gene_length_scaled": "counts_gene_length_scaled",
+            "counts_gene_scaled": "counts_gene_scaled", 
+            "tpm_transcript": "tpm_transcript", 
+            "counts_transcript": "counts_transcript", 
+            "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ]
+        )
+
+    emit: 
+        output_ch
+}
+VIASHMAIN
+nextflow run . -main-script "\$tempscript" &
+wait "\$!"
+
+VIASHEOF
+
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_TPM_GENE" ] && [ ! -e "$VIASH_PAR_TPM_GENE" ]; then
+  ViashError "Output file '$VIASH_PAR_TPM_GENE' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
+  ViashError "Output file '$VIASH_PAR_COUNTS_GENE' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ]; then
+  ViashError "Output file '$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_GENE_SCALED" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE_SCALED" ]; then
+  ViashError "Output file '$VIASH_PAR_COUNTS_GENE_SCALED' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_TPM_TRANSCRIPT" ] && [ ! -e "$VIASH_PAR_TPM_TRANSCRIPT" ]; then
+  ViashError "Output file '$VIASH_PAR_TPM_TRANSCRIPT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_LENGTHS_GENE" ] && [ ! -e "$VIASH_PAR_LENGTHS_GENE" ]; then
+  ViashError "Output file '$VIASH_PAR_LENGTHS_GENE' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && [ ! -e "$VIASH_PAR_COUNTS_TRANSCRIPT" ]; then
+  ViashError "Output file '$VIASH_PAR_COUNTS_TRANSCRIPT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_LENGTHS_TRANSCRIPT" ] && [ ! -e "$VIASH_PAR_LENGTHS_TRANSCRIPT" ]; then
+  ViashError "Output file '$VIASH_PAR_LENGTHS_TRANSCRIPT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT" ] && [ ! -e "$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT" ]; then
+  ViashError "Output file '$VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT' does not exist."
+  exit 1
+fi
+
+
+exit 0

target/executable/workflows/post_processing/.config.vsh.yaml

@@ -0,0 +1,513 @@
+name: "post_processing"
+namespace: "workflows"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "ID of the sample."
+    info: null
+    example:
+    - "foo"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\
+      \ or auto"
+    info: null
+    default:
+    - "auto"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fasta"
+    description: "Path to FASTA genome file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fai"
+    description: "Path to FASTA index"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "GTF file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam"
+    description: "Genome BAM file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--chrom_sizes"
+    description: "File containing chromosome lengths"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_multiqc"
+    description: "STAR align log file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_picard_args"
+    description: "Extra arguments to pass to picard MarkDuplicates command in addition\
+      \ to defaults defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_stringtie_args"
+    description: "Extra arguments to pass to stringtie command in addition to defaults\
+      \ defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--stringtie_ignore_gtf"
+    description: "Perform reference-guided de novo assembly of transcripts using StringTie,\
+      \ i.e. don't restrict to those in GTF file."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_bedtools_args"
+    description: "Extra arguments to pass to bedtools genomecov command in addition\
+      \ to defaults defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bam_csi_index"
+    description: "Create a CSI index for BAM files instead of the traditional BAI\
+      \ index. This will be required for genomes with larger chromosome sizes."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_mapped_reads"
+    description: "Minimum percentage of uniquely mapped reads below which samples\
+      \ are removed from further processing."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--with_umi"
+    description: "Enable UMI-based read deduplication."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_qc"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_markduplicates"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_stringtie"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_bigwig"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--processed_genome_bam"
+    info: null
+    default:
+    - "$id.markdup.sorted.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_index"
+    info: null
+    default:
+    - "$id.markdup.sorted.bam"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_stats"
+    info: null
+    default:
+    - "$id.markdup.sorted.bam.stats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_flagstat"
+    info: null
+    default:
+    - "$id.markdup.sorted.bam.flagstat"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_bam_idxstats"
+    info: null
+    default:
+    - "$id.markdup.sorted.bam.idxstats"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--markduplicates_metrics"
+    info: null
+    default:
+    - "$id.markdup.sorted.MarkDuplicates.metrics.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--stringtie_transcript_gtf"
+    info: null
+    default:
+    - "$id.stringtie.transcripts.gtf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--stringtie_coverage_gtf"
+    info: null
+    default:
+    - "$id.stringtie.coverage.gtf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--stringtie_abundance"
+    info: null
+    default:
+    - "$id.stringtie.gene_abundance.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--stringtie_ballgown"
+    info: null
+    default:
+    - "$id.stringtie.ballgown"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bedgraph_forward"
+    info: null
+    default:
+    - "$id.forward.bedgraph"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bedgraph_reverse"
+    info: null
+    default:
+    - "$id.reverse.bedgraph"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bigwig_forward"
+    info: null
+    default:
+    - "$id.forward.bigwig"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bigwig_reverse"
+    info: null
+    default:
+    - "$id.reverse.bigwig"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "A viash sub-workflow for the post-processing stage of nf-core/rnaseq\
+  \ pipeline.\n"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "picard_markduplicates"
+  repository:
+    type: "local"
+- name: "samtools/samtools_sort"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "samtools/samtools_index"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "samtools/samtools_stats"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "samtools/samtools_flagstat"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "samtools/samtools_idxstats"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "stringtie"
+  repository:
+    type: "local"
+- name: "bedtools_genomecov"
+  repository:
+    type: "local"
+- name: "ucsc/bedclip"
+  repository:
+    type: "local"
+- name: "ucsc/bedgraphtobigwig"
+  repository:
+    type: "local"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.1"
+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: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/post_processing/config.vsh.yaml"
+  runner: "executable"
+  engine: "native"
+  output: "target/executable/workflows/post_processing"
+  executable: "target/executable/workflows/post_processing/post_processing"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+  dependencies:
+  - "target/nextflow/picard_markduplicates"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_sort"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_index"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_flagstat"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_idxstats"
+  - "target/nextflow/stringtie"
+  - "target/nextflow/bedtools_genomecov"
+  - "target/nextflow/ucsc/bedclip"
+  - "target/nextflow/ucsc/bedgraphtobigwig"
+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"

target/executable/workflows/pre_processing/.config.vsh.yaml

@@ -0,0 +1,669 @@
+name: "pre_processing"
+namespace: "workflows"
+version: "main"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "ID of the sample."
+    info: null
+    example:
+    - "foo"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_1"
+    description: "Path to the sample (or read 1 of paired end sample)."
+    info: null
+    example:
+    - "input.fastq.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Path to read 2 of the sample."
+    info: null
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\
+      \ or auto"
+    info: null
+    default:
+    - "auto"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_index"
+    description: "BBsplit index"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_fasta_list"
+    description: "Path to comma-separated file containing a list of reference genomes\
+      \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
+      \ be explicitly set to \"false\". The file should contain 2 (comma separated)\
+      \ columns - short name and full path to reference genome(s)"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ribo_database_manifest"
+    description: "Text file containing paths to fasta files (one per line) that will\
+      \ be used to create the database for SortMeRNA."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcript_fasta"
+    description: "Path to FASTA transcriptome file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Path to GTF annotation file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--salmon_index"
+    description: "Path to directory containing the Salmon index"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--num_trimmed_reads"
+    description: "Number of reads after trimming"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Extra pipeline options"
+  arguments:
+  - type: "boolean"
+    name: "--skip_qc"
+    description: "Skip QC steps of the workflow."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "FastQC options"
+  arguments:
+  - type: "boolean"
+    name: "--skip_fastqc"
+    description: "Skip FatQC step."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "UMI-tools options"
+  arguments:
+  - type: "boolean"
+    name: "--with_umi"
+    description: "Enable UMI-based read deduplication."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_umi_extract"
+    description: "Skip umi_tools extract step."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_extract_method"
+    description: "UMI pattern to use."
+    info: null
+    default:
+    - "string"
+    required: false
+    choices:
+    - "string"
+    - "regex"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_bc_pattern"
+    description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
+      \ first 6 nucleotides of the read are from the UMI."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_bc_pattern2"
+    description: "The UMI barcode pattern to use if the UMI is located in read 2."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--umi_discard_read"
+    description: "After UMI barcode extraction discard either R1 or R2 by setting\
+      \ this parameter to 1 or 2, respectively."
+    info: null
+    default:
+    - 0
+    required: false
+    choices:
+    - 0
+    - 1
+    - 2
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_umi_separator"
+    description: "The character that separates the UMI in the read name. Most likely\
+      \ a colon if you skipped the extraction with UMI-tools and used other software."
+    info: null
+    default:
+    - "_"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--umitools_grouping_method"
+    description: "Method to use to determine read groups by subsuming those with similar\
+      \ UMIs. All methods start by identifying the reads with the same mapping position,\
+      \ but treat similar yet nonidentical UMIs differently."
+    info: null
+    default:
+    - "directional"
+    required: false
+    choices:
+    - "unique"
+    - "percentile"
+    - "cluster"
+    - "adjacency"
+    - "directional"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--save_umi_intermeds"
+    description: "If this option is specified, intermediate FastQ and BAM files produced\
+      \ by UMI-tools are also saved in the results directory."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Read trimming options"
+  arguments:
+  - type: "string"
+    name: "--trimmer"
+    description: "Specify the trimming tool to use."
+    info: null
+    default:
+    - "trimgalore"
+    required: false
+    choices:
+    - "trimgalore"
+    - "fastp"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_trimgalore_args"
+    description: "Extra arguments to pass to Trim Galore! command in addition to defaults\
+      \ defined by the pipeline."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_trimmed_reads"
+    description: "Minimum number of trimmed reads below which samples are removed\
+      \ from further processing. Some downstream steps in the pipeline will fail if\
+      \ this threshold is too low."
+    info: null
+    default:
+    - 10000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_trimming"
+    description: "Skip the adapter trimming step."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--save_trimmed"
+    description: "Save the trimmed FastQ files in the results directory."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Alignment options"
+  arguments:
+  - type: "string"
+    name: "--extra_salmon_quant_args"
+    description: "Extra arguments to pass to salmon quant command in addition to defaults\
+      \ defined by the pipeline."
+    info: null
+    default:
+    - ""
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Read filtering options"
+  arguments:
+  - type: "boolean"
+    name: "--skip_bbsplit"
+    description: "Skip BBSplit for removal of non-reference genome reads."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--remove_ribo_rna"
+    description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Other options"
+  arguments:
+  - type: "string"
+    name: "--extra_fq_subsample_args"
+    description: "Extra arguments to pass to fq subsample command in addition to defaults\
+      \ defined by the pipeline."
+    info: null
+    default:
+    - "--record-count 1000000 --seed 1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--qc_output1"
+    description: "Path to output directory"
+    info: null
+    default:
+    - "$id.$key.read_1.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--qc_output2"
+    description: "Path to output directory"
+    info: null
+    default:
+    - "$id.$key.read_2.fastq"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_html_1"
+    description: "FastQC HTML report for read 1."
+    info: null
+    default:
+    - "$id.read_1.fastqc.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_html_2"
+    description: "FastQC HTML report for read 2."
+    info: null
+    default:
+    - "$id.read_2.fastqc.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_zip_1"
+    description: "FastQC report archive for read 1."
+    info: null
+    default:
+    - "$id.read_1.fastqc.zip"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastqc_zip_2"
+    description: "FastQC report archive for read 2."
+    info: null
+    default:
+    - "$id.read_2.fastqc.zip"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_log_1"
+    info: null
+    default:
+    - "$id.read_1.trimming_report.txt"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_log_2"
+    info: null
+    default:
+    - "$id.read_2.trimming_report.txt"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_html_1"
+    info: null
+    default:
+    - "$id.read_1.trimmed_fastqc.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_html_2"
+    info: null
+    default:
+    - "$id.read_2.trimmed_fastqc.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_zip_1"
+    info: null
+    default:
+    - "$id.read_1.trimmed_fastqc.zip"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--trim_zip_2"
+    info: null
+    default:
+    - "$id.read_2.trimmed_fastqc.zip"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sortmerna_log"
+    description: "Sortmerna log file."
+    info: null
+    default:
+    - "$id.sortmerna.log"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--salmon_quant_output"
+    description: "Results from Salmon quant"
+    info: null
+    default:
+    - "$id.salmon_quant_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline.\n"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "fastqc"
+  repository:
+    type: "local"
+- name: "umitools/umitools_extract"
+  repository:
+    type: "local"
+- name: "trimgalore"
+  repository:
+    type: "local"
+- name: "bbmap_bbsplit"
+  repository:
+    type: "local"
+- name: "sortmerna"
+  repository:
+    type: "local"
+- name: "fastp"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+- name: "fq_subsample"
+  repository:
+    type: "local"
+- name: "salmon/salmon_quant"
+  repository:
+    type: "vsh"
+    repo: "vsh/biobox"
+    tag: "v0.1"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.1"
+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: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/pre_processing/config.vsh.yaml"
+  runner: "executable"
+  engine: "native"
+  output: "target/executable/workflows/pre_processing"
+  executable: "target/executable/workflows/pre_processing/pre_processing"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+  dependencies:
+  - "target/nextflow/fastqc"
+  - "target/nextflow/umitools/umitools_extract"
+  - "target/nextflow/trimgalore"
+  - "target/nextflow/bbmap_bbsplit"
+  - "target/nextflow/sortmerna"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/fastp"
+  - "target/nextflow/fq_subsample"
+  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
+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"

target/executable/workflows/prepare_genome/.config.vsh.yaml

@@ -0,0 +1,530 @@
+name: "prepare_genome"
+namespace: "workflows"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--fasta"
+    description: "Path to FASTA genome file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Path to GTF annotation file. This parameter is *mandatory* if --genome\
+      \ is not specified."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gff"
+    description: "Path to GFF3 annotation file. Required if \"--gtf\" is not specified."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--additional_fasta"
+    description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\
+      \ sequences."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcript_fasta"
+    description: "Path to FASTA transcriptome file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gene_bed"
+    description: "Path to BED file containing gene intervals. This will be created\
+      \ from the GTF file if not specified."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--splicesites"
+    description: "Splice sites file required for HISAT2."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--skip_bbsplit"
+    description: "Skip BBSplit for removal of non-reference genome reads."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_fasta_list"
+    description: "Path to comma-separated file containing a list of reference genomes\
+      \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
+      \ be explicitly set to \"false\". The file should contain 2 (comma separated)\
+      \ columns - short name and full path to reference genome(s)"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_index"
+    description: "Path to directory or tar.gz archive for pre-built STAR index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rsem_index"
+    description: "Path to directory or tar.gz archive for pre-built RSEM index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "extra_rsem_prepare_reference_args"
+    description: "Extra arguments to pass to rsem-prepare-reference command in addition\
+      \ to defaults defined by the pipeline."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--salmon_index"
+    description: "Path to directory or tar.gz archive for pre-built Salmon index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--kallisto_index"
+    description: "Path to directory or tar.gz archive for pre-built Kallisto index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_index"
+    description: "Path to directory or tar.gz archive for pre-built BBSplit index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--pseudo_aligner_kmer_size"
+    description: "Kmer length passed to indexing step of pseudoaligners."
+    info: null
+    default:
+    - 31
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--gencode"
+    description: "Specify if the GTF annotation is in GENCODE format."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--biotype"
+    description: "Biotype value to use while appending entries to GTF file when additional\
+      \ fasta file is provided."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--filter_gtf"
+    description: "Whether to filter the GTF or not?"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--aligner"
+    description: "Specifies the alignment algorithm to use - available options are\
+      \ 'star_salmon', 'star_rsem' and 'hisat2'."
+    info: null
+    default:
+    - "star_salmon"
+    required: false
+    choices:
+    - "star_salmon"
+    - "star_rsem"
+    - "hisat2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--pseudo_aligner"
+    description: "Specifies the pseudo aligner to use - available options are 'salmon'.\
+      \ Runs in addition to '--aligner'."
+    info: null
+    default:
+    - "salmon"
+    required: false
+    choices:
+    - "salmon"
+    - "kallisto"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fasta_uncompressed"
+    info: null
+    default:
+    - "reference_genome.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf_uncompressed"
+    info: null
+    default:
+    - "gene_annotation.gtf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcript_fasta_uncompressed"
+    info: null
+    default:
+    - "transcriptome.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gene_bed_uncompressed"
+    info: null
+    default:
+    - "gene_annotation.bed"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--star_index_uncompressed"
+    description: "Path to STAR index."
+    info: null
+    default:
+    - "STAR_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rsem_index_uncompressed"
+    description: "Path to directory or tar.gz archive for pre-built RSEM index."
+    info: null
+    default:
+    - "RSEM_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--salmon_index_uncompressed"
+    description: "Path to Salmon index."
+    info: null
+    default:
+    - "Salmon_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--kallisto_index_uncompressed"
+    description: "Path to Kallisto index."
+    info: null
+    default:
+    - "Kallisto_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bbsplit_index_uncompressed"
+    description: "Path to BBSplit index."
+    info: null
+    default:
+    - "BBSplit_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--chrom_sizes"
+    description: "File containing chromosome lengths"
+    info: null
+    default:
+    - "reference_genome.fasta.sizes"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fai"
+    description: "FASTA index file"
+    info: null
+    default:
+    - "reference_genome.fasta.fai"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "A subworkflow for preparing all the required genome references\n"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "gunzip"
+  repository:
+    type: "local"
+- name: "gffread"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
+- name: "cat_additional_fasta"
+  repository:
+    type: "local"
+- name: "gtf2bed"
+  repository:
+    type: "local"
+- name: "preprocess_transcripts_fasta"
+  repository:
+    type: "local"
+- name: "gtf_filter"
+  repository:
+    type: "local"
+- name: "rsem/rsem_prepare_reference"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
+- name: "getchromsizes"
+  repository:
+    type: "local"
+- name: "untar"
+  repository:
+    type: "vsh"
+    repo: "craftbox"
+    tag: "main"
+- name: "star/star_genome_generate"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
+- name: "bbmap_bbsplit"
+  repository:
+    type: "local"
+- name: "salmon/salmon_index"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
+- name: "kallisto/kallisto_index"
+  repository:
+    type: "local"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "biobox"
+  tag: "main"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "main"
+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: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/prepare_genome/config.vsh.yaml"
+  runner: "executable"
+  engine: "native"
+  output: "target/executable/workflows/prepare_genome"
+  executable: "target/executable/workflows/prepare_genome/prepare_genome"
+  viash_version: "0.9.0"
+  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+  dependencies:
+  - "target/nextflow/gunzip"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
+  - "target/nextflow/cat_additional_fasta"
+  - "target/nextflow/gtf2bed"
+  - "target/nextflow/preprocess_transcripts_fasta"
+  - "target/nextflow/gtf_filter"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
+  - "target/nextflow/getchromsizes"
+  - "target/dependencies/vsh/vsh/craftbox/main/nextflow/untar"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
+  - "target/nextflow/bbmap_bbsplit"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
+  - "target/nextflow/kallisto/kallisto_index"
+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"