Build branch main with version main (da414e7)

Build pipeline: viash-hub.biobox.main-7dwhr Source commit: da414e72c6 Source message: Add star solo component (#62) * add star solo component * change arguments from camelCase to snake_case * get rid of multiple_sep * drop star_solo component and just add arguments to star_align_reads * Update src/star/star_align_reads/script.py Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> --------- Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
2024-07-29 08:14:56 +00:00
parent ae3fef8eec
commit 02c1c9ebea
309 changed files with 58822 additions and 4148 deletions
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_collate"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -250,7 +264,7 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -513,10 +516,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_faidx"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -229,7 +243,7 @@ build_info:
  output: "target/executable/samtools/samtools_faidx"
  executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -506,10 +509,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -0,0 +1,459 @@
+name: "samtools_fasta"
+namespace: "samtools"
+version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input SAM/BAM/CRAM file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output FASTA file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--no_suffix"
+    alternatives:
+    - "-n"
+    description: "By default, either '/1' or '/2' is added to the end of read names\
+      \ where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes\
+      \ read names to be left as they are.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--suffix"
+    alternatives:
+    - "-N"
+    description: "Always add either '/1' or '/2' to the end of read names even when\
+      \ put into different files.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--use_oq"
+    alternatives:
+    - "-O"
+    description: "Use quality values from OQ tags in preference to standard quality\
+      \ string if available.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--singleton"
+    alternatives:
+    - "-s"
+    description: "write singleton reads to FILE."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--copy_tags"
+    alternatives:
+    - "-t"
+    description: "Copy RG, BC and QT tags to the FASTA header line, if they exist.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--copy_tags_list"
+    alternatives:
+    - "-T"
+    description: "Specify a comma-separated list of tags to copy to the FASTA header\
+      \ line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should\
+      \ be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted\
+      \ shell expansion.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--read1"
+    alternatives:
+    - "-1"
+    description: "Write reads with the READ1 FLAG set (and READ2 not set) to FILE\
+      \ instead of outputting them. \nIf the -s option is used, only paired reads\
+      \ will be written to this file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--read2"
+    alternatives:
+    - "-2"
+    description: "Write reads with the READ2 FLAG set (and READ1 not set) to FILE\
+      \ instead of outputting them. \nIf the -s option is used, only paired reads\
+      \ will be written to this file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_reads"
+    alternatives:
+    - "-o"
+    description: "Write reads with either READ1 FLAG or READ2 flag set to FILE instead\
+      \ of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_reads_both"
+    alternatives:
+    - "0"
+    description: "Write reads where the READ1 and READ2 FLAG bits set are either both\
+      \ set or both unset to FILE \ninstead of outputting them.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--filter_flags"
+    alternatives:
+    - "-f"
+    description: "Only output alignments with all bits set in INT present in the FLAG\
+      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0' \n(i.e. /^0[0-7]+/). Default: `0`.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--excl_flags"
+    alternatives:
+    - "-F"
+    description: "Do not output alignments with any bits set in INT present in the\
+      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0'\n(i.e. /^0[0-7]+/). This defaults to 0x900\
+      \ representing filtering of secondary and \nsupplementary alignments. Default:\
+      \ `0x900`.\n"
+    info: null
+    example:
+    - "0x900"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--incl_flags"
+    alternatives:
+    - "--rf"
+    description: "Only output alignments with any bits set in INT present in the FLAG\
+      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/),\
+      \ in octal by beginning with '0'\n(i.e. /^0[0-7]+/), as a decimal number not\
+      \ beginning with '0' or as a comma-separated list of \nflag names. Default:\
+      \ `0`.\n"
+    info: null
+    example:
+    - "0"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--excl_flags_all"
+    alternatives:
+    - "-G"
+    description: "Only EXCLUDE reads with all of the bits set in INT present in the\
+      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0' (i.e. /^0[0-7]+/).\nDefault: `0`.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--aux_tag"
+    alternatives:
+    - "-d"
+    description: "Only output alignments containing an auxiliary tag matching both\
+      \ TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types\
+      \ supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is\
+      \ comparable to the method used in samtools view --tag. The option may be specified\
+      \ \nmultiple times and is equivalent to using the --aux_tag_file option.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--aux_tag_file"
+    alternatives:
+    - "-D"
+    description: "Only output alignments containing an auxiliary tag matching TAG\
+      \ and having a value listed in FILE. \nThe format of the file is one line per\
+      \ value. This is equivalent to specifying --aux_tag multiple times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--casava"
+    alternatives:
+    - "-i"
+    description: "add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--compression"
+    alternatives:
+    - "-c"
+    description: "set compression level when writing gz or bgzf fasta files."
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index1"
+    alternatives:
+    - "--i1"
+    description: "write first index reads to FILE."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index2"
+    alternatives:
+    - "--i2"
+    description: "write second index reads to FILE."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--barcode_tag"
+    description: "Auxiliary tag to find index reads in. Default: `BC`.\n"
+    info: null
+    example:
+    - "BC"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quality_tag"
+    description: "Auxiliary tag to find index quality in. Default: `QT`.\n"
+    info: null
+    example:
+    - "QT"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--index_format"
+    description: "string to describe how to parse the barcode and quality tags. For\
+      \ example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters\
+      \ are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14\
+      \ characters for index 1.\nIf the tag contains a separator, then the numeric\
+      \ part can be replaced with`*` to mean \n'read until the separator or end of\
+      \ tag', for example: `n*i*`.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Converts a SAM, BAM or CRAM to FASTA format."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "fasta"
+- "bam"
+- "sam"
+- "cram"
+license: "MIT/Expat"
+references:
+  doi:
+  - "10.1093/bioinformatics/btp352"
+  - "10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/samtools"
+  homepage: "https://www.htslib.org/"
+  documentation: "https://www.htslib.org/doc/samtools-fasta.html"
+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/samtools:1.19.2--h50ea8bc_1"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \\\nsed 's#Using\
+      \ ##;s# \\([0-9\\.]*\\)$#: \\1#' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/samtools/samtools_fasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/samtools/samtools_fasta"
+  executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
+  viash_version: "0.9.0-RC6"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_fastq"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -77,8 +91,8 @@ argument_groups:
    alternatives:
    - "-T"
    description: "Specify a comma-separated list of tags to copy to the FASTQ header\
-      \ line, if they exist. \nTAGLIST can be blank or * to indicate all tags should\
-      \ be copied to the output. If using *, \nbe careful to quote it to avoid unwanted\
+      \ line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should\
+      \ be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted\
      \ shell expansion.\n"
    info: null
    required: false
@@ -144,10 +158,10 @@ argument_groups:
    alternatives:
    - "-f"
    description: "Only output alignments with all bits set in INT present in the FLAG\
-      \ field. INT can be specified \nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/)\
-      \ or in octal by beginning with `0' \n(i.e. /^0[0-7]+/).\n"
+      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0'\n(i.e. /^0[0-7]+/). Default: `0`.\n"
    info: null
-    default:
+    example:
    - 0
    required: false
    direction: "input"
@@ -158,12 +172,13 @@ argument_groups:
    alternatives:
    - "-F"
    description: "Do not output alignments with any bits set in INT present in the\
-      \ FLAG field. INT can be specified \nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/)\
-      \ or in octal by beginning with `0' \n(i.e. /^0[0-7]+/). This defaults to 0x900\
-      \ representing filtering of secondary and \nsupplementary alignments.\n"
+      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0' \n(i.e. /^0[0-7]+/). This defaults to 0x900\
+      \ representing filtering of secondary and \nsupplementary alignments. Default:\
+      \ `0x900`.\n"
    info: null
-    default:
-    - "2304"
+    example:
+    - "0x900"
    required: false
    direction: "input"
    multiple: false
@@ -173,11 +188,12 @@ argument_groups:
    alternatives:
    - "--rf"
    description: "Only output alignments with any bits set in INT present in the FLAG\
-      \ field. INT can be specified \nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),\
-      \ in octal by beginning with `0' \n(i.e. /^0[0-7]+/), as a decimal number not\
-      \ beginning with '0' or as a comma-separated list of \nflag names.\n"
+      \ field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/),\
+      \ in octal by beginning with '0'\n(i.e. /^0[0-7]+/), as a decimal number not\
+      \ beginning with '0' or as a comma-separated list of \nflag names. Default:\
+      \ `0`.\n"
    info: null
-    default:
+    example:
    - "0"
    required: false
    direction: "input"
@@ -188,10 +204,10 @@ argument_groups:
    alternatives:
    - "-G"
    description: "Only EXCLUDE reads with all of the bits set in INT present in the\
-      \ FLAG field. INT can be specified \nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/)\
-      \ or in octal by beginning with `0' \n(i.e. /^0[0-7]+/).\n"
+      \ FLAG field. INT can be specified \nin hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/)\
+      \ or in octal by beginning with '0' (i.e. /^0[0-7]+/).\nDefault: `0`.\n"
    info: null
-    default:
+    example:
    - 0
    required: false
    direction: "input"
@@ -227,7 +243,7 @@ argument_groups:
    name: "--casava"
    alternatives:
    - "-i"
-    description: "add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
+    description: "Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.\n"
    info: null
    direction: "input"
  - type: "integer"
@@ -236,7 +252,7 @@ argument_groups:
    - "-c"
    description: "set compression level when writing gz or bgzf fastq files."
    info: null
-    default:
+    example:
    - 0
    required: false
    direction: "input"
@@ -268,9 +284,9 @@ argument_groups:
    multiple_sep: ";"
  - type: "string"
    name: "--barcode_tag"
-    description: "Auxiliary tag to find index reads in."
+    description: "Auxiliary tag to find index reads in. Default: `BC`.\n"
    info: null
-    default:
+    example:
    - "BC"
    required: false
    direction: "input"
@@ -278,9 +294,9 @@ argument_groups:
    multiple_sep: ";"
  - type: "string"
    name: "--quality_tag"
-    description: "Auxiliary tag to find index quality in."
+    description: "Auxiliary tag to find index quality in. Default: `QT`.\n"
    info: null
-    default:
+    example:
    - "QT"
    required: false
    direction: "input"
@@ -289,11 +305,11 @@ argument_groups:
  - type: "string"
    name: "--index_format"
    description: "string to describe how to parse the barcode and quality tags. For\
-      \ example:\n[i14i8]: the first 14 characters are index 1, the next 8 characters\
-      \ are index 2.\n[n8i14]: ignore the first 8 characters, and use the next 14\
+      \ example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters\
+      \ are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14\
      \ characters for index 1.\nIf the tag contains a separator, then the numeric\
      \ part can be replaced with '*' to mean \n'read until the separator or end of\
-      \ tag', for example: [n*i*].\n"
+      \ tag', for example: `n*i*`.\n"
    info: null
    required: false
    direction: "input"
@@ -417,7 +433,7 @@ build_info:
  output: "target/executable/samtools/samtools_fastq"
  executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -215,8 +218,8 @@ function ViashHelp {
  echo "        type: string"
  echo "        Specify a comma-separated list of tags to copy to the FASTQ header line,"
  echo "        if they exist."
-  echo "        TAGLIST can be blank or * to indicate all tags should be copied to the"
-  echo "        output. If using *,"
+  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
+  echo "        output. If using \`*\`,"
  echo "        be careful to quote it to avoid unwanted shell expansion."
  echo ""
  echo "    -1, --read1"
@@ -247,43 +250,43 @@ function ViashHelp {
  echo ""
  echo "    -f, --filter_flags"
  echo "        type: integer"
-  echo "        default: 0"
+  echo "        example: 0"
  echo "        Only output alignments with all bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
-  echo "        in hex by beginning with \`0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with \`0'"
-  echo "        (i.e. /^0[0-7]+/)."
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
  echo ""
  echo "    -F, --excl_flags"
  echo "        type: string"
-  echo "        default: 2304"
+  echo "        example: 0x900"
  echo "        Do not output alignments with any bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
-  echo "        in hex by beginning with \`0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with \`0'"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
  echo "        secondary and"
-  echo "        supplementary alignments."
+  echo "        supplementary alignments. Default: \`0x900\`."
  echo ""
  echo "    --rf, --incl_flags"
  echo "        type: string"
-  echo "        default: 0"
+  echo "        example: 0"
  echo "        Only output alignments with any bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
-  echo "        in hex by beginning with \`0x' (i.e. /^0x[0-9A-F]+/), in octal by"
-  echo "        beginning with \`0'"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
+  echo "        beginning with '0'"
  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
  echo "        comma-separated list of"
-  echo "        flag names."
+  echo "        flag names. Default: \`0\`."
  echo ""
  echo "    -G, --excl_flags_all"
  echo "        type: integer"
-  echo "        default: 0"
+  echo "        example: 0"
  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
-  echo "        in hex by beginning with \`0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with \`0'"
-  echo "        (i.e. /^0[0-7]+/)."
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
+  echo "        Default: \`0\`."
  echo ""
  echo "    -d, --aux_tag"
  echo "        type: string"
@@ -304,11 +307,12 @@ function ViashHelp {
  echo ""
  echo "    -i, --casava"
  echo "        type: boolean_true"
-  echo "        add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
+  echo "        Add Illumina Casava 1.8 format entry to header, for example:"
+  echo "        \`1:N:0:ATCACG\`."
  echo ""
  echo "    -c, --compression"
  echo "        type: integer"
-  echo "        default: 0"
+  echo "        example: 0"
  echo "        set compression level when writing gz or bgzf fastq files."
  echo ""
  echo "    --i1, --index1"
@@ -321,25 +325,25 @@ function ViashHelp {
  echo ""
  echo "    --barcode_tag"
  echo "        type: string"
-  echo "        default: BC"
-  echo "        Auxiliary tag to find index reads in."
+  echo "        example: BC"
+  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
  echo ""
  echo "    --quality_tag"
  echo "        type: string"
-  echo "        default: QT"
-  echo "        Auxiliary tag to find index quality in."
+  echo "        example: QT"
+  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
  echo ""
  echo "    --index_format"
  echo "        type: string"
  echo "        string to describe how to parse the barcode and quality tags. For"
  echo "        example:"
-  echo "        [i14i8]: the first 14 characters are index 1, the next 8 characters are"
-  echo "        index 2."
-  echo "        [n8i14]: ignore the first 8 characters, and use the next 14 characters"
+  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
+  echo "        are index 2."
+  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
  echo "        for index 1."
  echo "        If the tag contains a separator, then the numeric part can be replaced"
  echo "        with '*' to mean"
-  echo "        'read until the separator or end of tag', for example: [n*i*]."
+  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
 }

 # initialise variables
@@ -619,10 +623,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1311,30 +1316,9 @@ fi
 if [ -z ${VIASH_PAR_COPY_TAGS+x} ]; then
  VIASH_PAR_COPY_TAGS="false"
 fi
-if [ -z ${VIASH_PAR_FILTER_FLAGS+x} ]; then
-  VIASH_PAR_FILTER_FLAGS="0"
-fi
-if [ -z ${VIASH_PAR_EXCL_FLAGS+x} ]; then
-  VIASH_PAR_EXCL_FLAGS="2304"
-fi
-if [ -z ${VIASH_PAR_INCL_FLAGS+x} ]; then
-  VIASH_PAR_INCL_FLAGS="0"
-fi
-if [ -z ${VIASH_PAR_EXCL_FLAGS_ALL+x} ]; then
-  VIASH_PAR_EXCL_FLAGS_ALL="0"
-fi
 if [ -z ${VIASH_PAR_CASAVA+x} ]; then
  VIASH_PAR_CASAVA="false"
 fi
-if [ -z ${VIASH_PAR_COMPRESSION+x} ]; then
-  VIASH_PAR_COMPRESSION="0"
-fi
-if [ -z ${VIASH_PAR_BARCODE_TAG+x} ]; then
-  VIASH_PAR_BARCODE_TAG="BC"
-fi
-if [ -z ${VIASH_PAR_QUALITY_TAG+x} ]; then
-  VIASH_PAR_QUALITY_TAG="QT"
-fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1671,7 +1655,14 @@ set -e
 [[ "\$par_copy_tags" == "false" ]] && unset par_copy_tags
 [[ "\$par_casava" == "false" ]] && unset par_casava

-samtools fastq \\
+if [[ "\$meta_name" == "samtools_fasta" ]]; then
+  subcommand=fasta
+elif [[ "\$meta_name" == "samtools_fastq" ]]; then
+  subcommand=fastq
+else
+  echo "Unrecognized component name" && exit 1
+fi
+samtools "\$subcommand" \\
    \${par_no_suffix:+-n} \\
    \${par_suffix:+-N} \\
    \${par_use_oq:+-O} \\
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_flagstat"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -159,7 +173,7 @@ build_info:
  output: "target/executable/samtools/samtools_flagstat"
  executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -468,10 +471,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_idxstats"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -169,7 +183,7 @@ build_info:
  output: "target/executable/samtools/samtools_idxstats"
  executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -472,10 +475,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_index"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -175,7 +189,7 @@ build_info:
  output: "target/executable/samtools/samtools_index"
  executable: "target/executable/samtools/samtools_index/samtools_index"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -479,10 +482,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_sort"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -318,7 +332,7 @@ build_info:
  output: "target/executable/samtools/samtools_sort"
  executable: "target/executable/samtools/samtools_sort/samtools_sort"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -550,10 +553,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_stats"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -38,12 +52,16 @@ argument_groups:
    name: "--coverage"
    alternatives:
    - "-c"
-    description: "Coverage distribution min,max,step [1,1000,1].\n"
+    description: "Coverage distribution min;max;step. Default: [1, 1000, 1].\n"
    info: null
+    example:
+    - 1
+    - 1000
+    - 1
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "boolean_true"
    name: "--remove_dups"
    alternatives:
@@ -62,9 +80,10 @@ argument_groups:
    name: "--required_flag"
    alternatives:
    - "-f"
-    description: "Required flag, 0 for unset. See also `samtools flags`.\n"
+    description: "Required flag, 0 for unset. See also `samtools flags`. Default:\
+      \ `\"0\"`.\n"
    info: null
-    default:
+    example:
    - "0"
    required: false
    direction: "input"
@@ -74,9 +93,10 @@ argument_groups:
    name: "--filtering_flag"
    alternatives:
    - "-F"
-    description: "Filtering flag, 0 for unset. See also `samtools flags`.\n"
+    description: "Filtering flag, 0 for unset. See also `samtools flags`. Default:\
+      \ `0`.\n"
    info: null
-    default:
+    example:
    - "0"
    required: false
    direction: "input"
@@ -85,9 +105,9 @@ argument_groups:
  - type: "double"
    name: "--GC_depth"
    description: "The size of GC-depth bins (decreasing bin size increases memory\
-      \ requirement).\n"
+      \ requirement). Default: `20000`.\n"
    info: null
-    default:
+    example:
    - 20000.0
    required: false
    direction: "input"
@@ -97,9 +117,9 @@ argument_groups:
    name: "--insert_size"
    alternatives:
    - "-i"
-    description: "Maximum insert size.\n"
+    description: "Maximum insert size. Default: `8000`.\n"
    info: null
-    default:
+    example:
    - 8000
    required: false
    direction: "input"
@@ -119,9 +139,10 @@ argument_groups:
    name: "--read_length"
    alternatives:
    - "-l"
-    description: "Include in the statistics only reads with the given read length.\n"
+    description: "Include in the statistics only reads with the given read length.\
+      \ Default: `-1`.\n"
    info: null
-    default:
+    example:
    - -1
    required: false
    direction: "input"
@@ -131,9 +152,9 @@ argument_groups:
    name: "--most_inserts"
    alternatives:
    - "-m"
-    description: "Report only the main part of inserts.\n"
+    description: "Report only the main part of inserts. Default: `0.99`.\n"
    info: null
-    default:
+    example:
    - 0.99
    required: false
    direction: "input"
@@ -154,9 +175,9 @@ argument_groups:
    name: "--trim_quality"
    alternatives:
    - "-q"
-    description: "The BWA trimming parameter.\n"
+    description: "The BWA trimming parameter. Default: `0`.\n"
    info: null
-    default:
+    example:
    - 0
    required: false
    direction: "input"
@@ -218,9 +239,9 @@ argument_groups:
    alternatives:
    - "-g"
    description: "Only bases with coverage above this value will be included in the\
-      \ target percentage computation.\n"
+      \ target percentage computation. Default: `0`.\n"
    info: null
-    default:
+    example:
    - 0
    required: false
    direction: "input"
@@ -253,7 +274,7 @@ argument_groups:
    - "-o"
    description: "Output file.\n"
    info: null
-    default:
+    example:
    - "out.txt"
    must_exist: true
    create_parent: true
@@ -380,7 +401,7 @@ build_info:
  output: "target/executable/samtools/samtools_stats"
  executable: "target/executable/samtools/samtools_stats/samtools_stats"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -190,7 +193,8 @@ function ViashHelp {
  echo ""
  echo "    -c, --coverage"
  echo "        type: integer, multiple values allowed"
-  echo "        Coverage distribution min,max,step [1,1000,1]."
+  echo "        example: 1;1000;1"
+  echo "        Coverage distribution min;max;step. Default: [1, 1000, 1]."
  echo ""
  echo "    -d, --remove_dups"
  echo "        type: boolean_true"
@@ -202,24 +206,24 @@ function ViashHelp {
  echo ""
  echo "    -f, --required_flag"
  echo "        type: string"
-  echo "        default: 0"
-  echo "        Required flag, 0 for unset. See also \`samtools flags\`."
+  echo "        example: 0"
+  echo "        Required flag, 0 for unset. See also \`samtools flags\`. Default: \`\"0\"\`."
  echo ""
  echo "    -F, --filtering_flag"
  echo "        type: string"
-  echo "        default: 0"
-  echo "        Filtering flag, 0 for unset. See also \`samtools flags\`."
+  echo "        example: 0"
+  echo "        Filtering flag, 0 for unset. See also \`samtools flags\`. Default: \`0\`."
  echo ""
  echo "    --GC_depth"
  echo "        type: double"
-  echo "        default: 20000.0"
+  echo "        example: 20000.0"
  echo "        The size of GC-depth bins (decreasing bin size increases memory"
-  echo "        requirement)."
+  echo "        requirement). Default: \`20000\`."
  echo ""
  echo "    -i, --insert_size"
  echo "        type: integer"
-  echo "        default: 8000"
-  echo "        Maximum insert size."
+  echo "        example: 8000"
+  echo "        Maximum insert size. Default: \`8000\`."
  echo ""
  echo "    -I, --id"
  echo "        type: string"
@@ -227,13 +231,14 @@ function ViashHelp {
  echo ""
  echo "    -l, --read_length"
  echo "        type: integer"
-  echo "        default: -1"
+  echo "        example: -1"
  echo "        Include in the statistics only reads with the given read length."
+  echo "        Default: \`-1\`."
  echo ""
  echo "    -m, --most_inserts"
  echo "        type: double"
-  echo "        default: 0.99"
-  echo "        Report only the main part of inserts."
+  echo "        example: 0.99"
+  echo "        Report only the main part of inserts. Default: \`0.99\`."
  echo ""
  echo "    -P, --split_prefix"
  echo "        type: string"
@@ -242,8 +247,8 @@ function ViashHelp {
  echo ""
  echo "    -q, --trim_quality"
  echo "        type: integer"
-  echo "        default: 0"
-  echo "        The BWA trimming parameter."
+  echo "        example: 0"
+  echo "        The BWA trimming parameter. Default: \`0\`."
  echo ""
  echo "    -r, --ref_seq"
  echo "        type: file, file must exist"
@@ -270,9 +275,9 @@ function ViashHelp {
  echo ""
  echo "    -g, --cov_threshold"
  echo "        type: integer"
-  echo "        default: 0"
+  echo "        example: 0"
  echo "        Only bases with coverage above this value will be included in the target"
-  echo "        percentage computation."
+  echo "        percentage computation. Default: \`0\`."
  echo ""
  echo "    --input_fmt_option"
  echo "        type: string"
@@ -286,7 +291,7 @@ function ViashHelp {
  echo "Outputs:"
  echo "    -o, --output"
  echo "        type: file, required parameter, output, file must exist"
-  echo "        default: out.txt"
+  echo "        example: out.txt"
  echo "        Output file."
 }

@@ -567,10 +572,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -734,7 +740,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_COVERAGE" ]; then
              VIASH_PAR_COVERAGE="$2"
            else
-              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE,""$2"
+              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --coverage. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -743,7 +749,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_COVERAGE" ]; then
              VIASH_PAR_COVERAGE=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -751,7 +757,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_COVERAGE" ]; then
              VIASH_PAR_COVERAGE="$2"
            else
-              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE,""$2"
+              VIASH_PAR_COVERAGE="$VIASH_PAR_COVERAGE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -1246,36 +1252,12 @@ fi
 if [ -z ${VIASH_PAR_CUSTOMIZED_INDEX_FILE+x} ]; then
  VIASH_PAR_CUSTOMIZED_INDEX_FILE="false"
 fi
-if [ -z ${VIASH_PAR_REQUIRED_FLAG+x} ]; then
-  VIASH_PAR_REQUIRED_FLAG="0"
-fi
-if [ -z ${VIASH_PAR_FILTERING_FLAG+x} ]; then
-  VIASH_PAR_FILTERING_FLAG="0"
-fi
-if [ -z ${VIASH_PAR_GC_DEPTH+x} ]; then
-  VIASH_PAR_GC_DEPTH="20000.0"
-fi
-if [ -z ${VIASH_PAR_INSERT_SIZE+x} ]; then
-  VIASH_PAR_INSERT_SIZE="8000"
-fi
-if [ -z ${VIASH_PAR_READ_LENGTH+x} ]; then
-  VIASH_PAR_READ_LENGTH="-1"
-fi
-if [ -z ${VIASH_PAR_MOST_INSERTS+x} ]; then
-  VIASH_PAR_MOST_INSERTS="0.99"
-fi
-if [ -z ${VIASH_PAR_TRIM_QUALITY+x} ]; then
-  VIASH_PAR_TRIM_QUALITY="0"
-fi
 if [ -z ${VIASH_PAR_SPARSE+x} ]; then
  VIASH_PAR_SPARSE="false"
 fi
 if [ -z ${VIASH_PAR_REMOVE_OVERLAPS+x} ]; then
  VIASH_PAR_REMOVE_OVERLAPS="false"
 fi
-if [ -z ${VIASH_PAR_COV_THRESHOLD+x} ]; then
-  VIASH_PAR_COV_THRESHOLD="0"
-fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1305,7 +1287,7 @@ fi

 # check whether parameters values are of the right type
 if [ -n "$VIASH_PAR_COVERAGE" ]; then
-  IFS=','
+  IFS=';'
  set -f
  for val in $VIASH_PAR_COVERAGE; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
@@ -1619,6 +1601,9 @@ set -e
 [[ "\$par_sparse" == "false" ]] && unset par_sparse
 [[ "\$par_remove_overlaps" == "false" ]] && unset par_remove_overlaps

+# change the coverage input from X;X;X to X,X,X
+par_coverage=\$(echo "\$par_coverage" | tr ';' ',')
+
 samtools stats \\
    \${par_coverage:+-c "\$par_coverage"} \\
    \${par_remove_dups:+-d} \\
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -1,6 +1,20 @@
 name: "samtools_view"
 namespace: "samtools"
 version: "main"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -651,7 +665,7 @@ build_info:
  output: "target/executable/samtools/samtools_view"
  executable: "target/executable/samtools/samtools_view/samtools_view"
  viash_version: "0.9.0-RC6"
-  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -10,6 +10,9 @@
 # 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.
+# 
+# Component authors:
+#  * Emma Rousseau (author, maintainer)

 set -e

@@ -819,10 +822,11 @@ ENTRYPOINT []
 RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

+LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z"
+LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
+LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER