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biobox/target/executable/samtools/samtools_view/.config.vsh.yaml
CI fbfdc19532 Build branch qualimap with version qualimap (e6420cd) 
Build pipeline: viash-hub.biobox.qualimap-hcs27

Source commit: e6420cd80f

Source message: update unit tests
2024-07-29 14:59:23 +00:00

678 lines
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name: "samtools_view"
namespace: "samtools"
version: "qualimap"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
description: "Input SAM, BAM, or CRAM file."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fai_reference"
alternatives:
- "-t"
description: "A tab-delimited FILE. Each line must contain the reference name\
\ in the first column\nand the length of the reference in the second column,\
\ with one line for each distinct\nreference. Any additional fields beyond the\
\ second column are ignored. This file also\ndefines the order of the reference\
\ sequences in sorting. If you run: `samtools faidx <ref.fa>',\nthe resulting\
\ index file <ref.fa>.fai can be used as this FILE.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--reference"
alternatives:
- "-T"
description: "A FASTA format reference FILE, optionally compressed by bgzip and\
\ ideally indexed by samtools faidx.\nIf an index is not present one will be\
\ generated for you, if the reference file is local.\nIf the reference file\
\ is not local, but is accessed instead via an https://, s3:// or other URL,\n\
the index file will need to be supplied by the server alongside the reference.\
\ It is possible to\nhave the reference and index files in different locations\
\ by supplying both to this option separated\nby the string \"##idx##\", for\
\ example:\n--reference ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai\n\
However, note that only the location of the reference will be stored in the\
\ output file header.\nIf this method is used to make CRAM files, the cram reader\
\ may not be able to find the index,\nand may not be able to decode the file\
\ unless it can get the references it needs using a different\nmethod.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--target_file"
alternatives:
- "-L"
description: "Only output alignments overlapping the input BED FILE [null].\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--region_file"
description: "Use an index and multi-region iterator to only output alignments\
\ overlapping the input BED FILE.\nEquivalent to --use_index --target_file FILE.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--qname_file"
alternatives:
- "-N"
description: "Output only alignments with read names listed in FILE. If FILE starts\
\ with ^ then the operation is\nnegated and only outputs alignment with read\
\ groups not listed in FILE. It is not permissible to mix\nboth the filter-in\
\ and filter-out style syntax in the same command.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_group_file"
alternatives:
- "-R"
description: "Output alignments in read groups listed in FILE [null]. If FILE\
\ starts with ^ then the operation is\nnegated and only outputs alignment with\
\ read names not listed in FILE. It is not permissible to mix\nboth the filter-in\
\ and filter-out style syntax in the same command. Note that records with no\
\ RG tag\nwill also be output when using this option. This behaviour may change\
\ in a future release.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--use_index"
alternatives:
- "-M"
description: "Use the multi-region iterator on the union of a BED file and command-line\
\ region arguments.\nThis avoids re-reading the same regions of files so can\
\ sometimes be much faster. Note this also\nremoves duplicate sequences. Without\
\ this a sequence that overlaps multiple regions specified on\nthe command line\
\ will be reported multiple times. The usage of a BED file is optional and its\
\ path\nhas to be preceded by --target_file option.\n"
info: null
direction: "input"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output to FILE instead of [stdout]."
info: null
example:
- "output.bam"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--bam"
alternatives:
- "-b"
description: "Output in the BAM format."
info: null
direction: "input"
- type: "boolean_true"
name: "--cram"
alternatives:
- "-C"
description: "Output in the CRAM format (requires --reference).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--fast"
description: "Enable fast compression. This also changes the default output format\
\ to BAM,\nbut this can be overridden by the explicit format options or using\
\ a filename\nwith a known suffix.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--uncompressed"
alternatives:
- "-u"
description: "Output uncompressed data. This also changes the default output format\
\ to BAM,\nbut this can be overridden by the explicit format options or using\
\ a filename\nwith a known suffix.\nThis option saves time spent on compression/decompression\
\ and is thus preferred\nwhen the output is piped to another samtools command.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--with_header"
description: "Include the header in the output.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--header_only"
alternatives:
- "-H"
description: "Output the header only.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_header"
description: "When producing SAM format, output alignment records but not headers.\n\
This is the default; the option can be used to reset the effect of \n--with_header/--header_only.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--count"
alternatives:
- "-c"
description: "Instead of printing the alignments, only count them and print the\
\ total number.\nAll filter options, such as --require_flags, --excl_flags,\
\ and --min_MQ, are taken\ninto account. The --unmap option is ignored in this\
\ mode.\n"
info: null
direction: "input"
- type: "file"
name: "--output_unselected"
alternatives:
- "-U"
description: "Write alignments that are not selected by the various filter options\
\ to FILE.\nWhen this option is used, all alignments (or all alignments intersecting\
\ the regions\nspecified) are written to either the output file or this file,\
\ but never both.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--unmap"
alternatives:
- "-p"
description: "Set the UNMAP flag on alignments that are not selected by the filter\
\ options.\nThese alignments are then written to the normal output. This is\
\ not compatible\nwith --output_unselected.\n"
info: null
direction: "input"
- type: "string"
name: "--read_group"
alternatives:
- "-r"
description: "Output alignments in read group STR [null]. Note that records with\
\ no RG tag will also be output\nwhen using this option. This behaviour may\
\ change in a future release.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--tag"
alternatives:
- "-d"
description: "Only output alignments with tag STR1 and associated value STR2,\
\ which can be a string or an integer\n[null].\nThe value can be omitted, in\
\ which case only the tag is considered.\nNote that this option does not specify\
\ a tag type. For example, use --tag XX:42 to select alignments\nwith an XX:i:42\
\ field, not --tag XX:i:42.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tag_file"
alternatives:
- "-D"
description: "Only output alignments with tag STR and associated values listed\
\ in FILE.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_MQ"
alternatives:
- "-q"
description: "Skip alignments with MAPQ smaller than INT.\n"
info: null
default:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--library"
alternatives:
- "-l"
description: "Only output alignments in library STR.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_qlen"
alternatives:
- "-m"
description: "Only output alignments with number of CIGAR bases consuming query\
\ sequence >= INT.\n"
info: null
default:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--expr"
alternatives:
- "-e"
description: "Only include alignments that match the filter expression STR. The\
\ syntax for these expressions is\ndescribed in the main samtools.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--require_flags"
alternatives:
- "-f"
description: "Only output alignments with all bits set in FLAG present in the\
\ FLAG field. FLAG can be specified\nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),\
\ in octal by beginning with `0' (i.e. /^0[0-7]+/),\nas a decimal number not\
\ beginning with '0' or as a comma-separated list of flag names.\n"
info: null
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 FLAG present in the\
\ FLAG field. FLAG can be specified\nin hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),\
\ in octal by beginning with `0' (i.e. /^0[0-7]+/),\nas a decimal number not\
\ beginning with '0' or as a comma-separated list of flag names.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--excl_all_flags"
alternatives:
- "-G"
description: "Do not output alignments with all bits set in INT present in the\
\ FLAG field. This is the opposite of\n--require_flags such that --require_flags\
\ 12 --exclude_all_flags 12 is the same as no filtering at all.\nFLAG can be\
\ specified in 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 flag names.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--incl_flags"
alternatives:
- "--rf"
description: "Only output alignments with any bit set in FLAG present in the FLAG\
\ field. FLAG can be specified in hex\nby beginning with `0x' (i.e. /^0x[0-9A-F]+/),\
\ in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal\nnumber not\
\ beginning with '0' or as a comma-separated list of flag names.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--remove_tag"
alternatives:
- "-x"
description: "Read tag(s) to exclude from output (repeatable) [null]. This can\
\ be a single tag or a comma separated list.\nAlternatively the option itself\
\ can be repeated multiple times.\nIf the list starts with a `^' then it is\
\ negated and treated as a request to remove all tags except those in STR.\n\
The list may be empty, so --remove_tag ^ will remove all tags.\nNote that tags\
\ will only be removed from reads that pass filtering.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--keep_tag"
description: "This keeps only tags listed in STR and is directly equivalent to\
\ --remove_tag ^STR. Specifying an empty list\nwill remove all tags. If both\
\ --keep_tag and --remove_tag are specified then --keep_tag has precedence.\n\
Note that tags will only be removed from reads that pass filtering.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--remove_B"
alternatives:
- "-B"
description: "Collapse the backward CIGAR operation.\n"
info: null
direction: "input"
- type: "string"
name: "--add_flags"
description: "Adds flag(s) to read. FLAG can be specified in hex by beginning\
\ with `0x' (i.e. /^0x[0-9A-F]+/), in octal\nby beginning with `0' (i.e. /^0[0-7]+/),\
\ as a decimal number not beginning with '0' or as a comma-separated\nlist of\
\ flag names.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--remove_flags"
description: "Remove flag(s) from read. FLAG is specified in the same way as with\
\ the --add_flags option.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--subsample"
description: "Output only a proportion of the input alignments, as specified by\
\ 0.0 <= FLOAT <= 1.0, which gives the fraction\nof templates/pairs to be kept.\
\ This subsampling acts in the same way on all of the alignment records in the\
\ same\ntemplate or read pair, so it never keeps a read but not its mate.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--subsample_seed"
description: "Subsampling seed used to influence which subset of reads is kept.\
\ When subsampling data that has previously\nbeen subsampled, be sure to use\
\ a different seed value from those used previously; otherwise more reads will\n\
be retained than expected.\n"
info: null
default:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--fetch_pairs"
alternatives:
- "-P"
description: "Retrieve pairs even when the mate is outside of the requested region.\
\ Enabling this option also turns on the\nmulti-region iterator (-M). A region\
\ to search must be specified, either on the command-line, or using the\n--target_file\
\ option. The input file must be an indexed regular file.\nThis option first\
\ scans the requested region, using the RNEXT and PNEXT fields of the records\
\ that have the\nPAIRED flag set and pass other filtering options to find where\
\ paired reads are located. These locations are\nused to build an expanded region\
\ list, and a set of QNAMEs to allow from the new regions. It will then make\n\
a second pass, collecting all reads from the originally-specified region list\
\ together with reads from additional\nlocations that match the allowed set\
\ of QNAMEs. Any other filtering options used will be applied to all reads\n\
found during this second pass.\nAs this option links reads using RNEXT and PNEXT,\
\ it is important that these fields are set accurately. Use\n'samtools fixmate'\
\ to correct them if necessary.\nNote that this option does not work with the\
\ --count, --output-unselected or --unmap options.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--customized_index"
alternatives:
- "-X"
description: "Include customized index file as a part of arguments. See EXAMPLES\
\ section for sample of usage.\n"
info: null
direction: "input"
- type: "string"
name: "--sanitize"
alternatives:
- "-z"
description: "Perform some sanity checks on the state of SAM record fields, fixing\
\ up common mistakes made by aligners.\nThese include soft-clipping alignments\
\ when they extend beyond the end of the reference, marking records as\nunmapped\
\ when they have reference * or position 0, and ensuring unmapped alignments\
\ have no CIGAR or mapping\nquality for unmapped alignments and no MD, NM, CG\
\ or SM tags.\nFLAGs is a comma-separated list of keywords chosen from the following\
\ list.\n\nunmap: The UNMAPPED BAM flag. This is set for reads with position\
\ <= 0, reference name \"*\" or reads starting\nbeyond the end of the reference.\
\ Note CIGAR \"*\" is permitted for mapped data so does not trigger this.\n\n\
pos: Position and reference name fields. These may be cleared when a sequence\
\ is unmapped due to the\ncoordinates being beyond the end of the reference.\
\ Selecting this may change the sort order of the file,\nso it is not a part\
\ of the on compound argument.\nmqual: Mapping quality. This is set to zero\
\ for unmapped reads.\ncigar: Modifies CIGAR fields, either by adding soft-clips\
\ for reads that overlap the end of the reference or\n by clearing it\
\ for unmapped reads.\naux: For unmapped data, some auxiliary fields are meaningless\
\ and will be removed. These include NM, MD, CG and SM.\noff: Perform no sanity\
\ fixing. This is the default\non: Sanitize data in a way that guarantees the\
\ same sort order. This is everything except for pos.\nall: All sanitizing options,\
\ including pos.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--no_PG"
description: "Do not add a @PG line to the header of the output file.\n"
info: null
direction: "input"
- type: "string"
name: "--input_fmt_option"
description: "Specify a single input file format option in the form of OPTION\
\ or OPTION=VALUE.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--output_fmt"
alternatives:
- "-O"
description: "Specify output format (SAM, BAM, CRAM).\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--output_fmt_option"
description: "Specify a single output file format option in the form of OPTION\
\ or OPTION=VALUE.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--write_index"
description: "Automatically index the output files.\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Views and converts SAM/BAM/CRAM files."
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_data"
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "view"
- "convert"
- "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-view.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: "qualimap"
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_view/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/samtools/samtools_view"
executable: "target/executable/samtools/samtools_view/samtools_view"
viash_version: "0.9.0-RC6"
git_commit: "e6420cd80f226128b7223ff79ce1297f99993657"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "qualimap"
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 := 'qualimap'"
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"
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