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0075a8df9361b042ca890c1eef14ad700bd00a5d
biobox/target/executable/gffread/.config.vsh.yaml
CI 0075a8df93 Build branch main with version main (8fe9d66) 
Build pipeline: viash-hub.biobox.main-vhhxn

Source commit: 8fe9d66b0c

Source message: Bcftools stats (#142)

* Initial Commit

* Adding options to config

* Update on script

* update

* Adding test 2 and 3

* Update on config and test

* adding more tests

* debugging and adding tests

* Adding last tests

* removing test_data dir

* Update CHANGELOG.md

* small changes

* small change in help file

* Requested changes

---------

Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
2024-09-10 14:10:14 +00:00

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name: "gffread"
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: "A reference file in either the GFF3, GFF2 or GTF format.\n"
info: null
example:
- "annotation.gff"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--chr_mapping"
alternatives:
- "-m"
description: "<chr_replace> is a name mapping table for converting reference sequence\
\ names, \nhaving this 2-column format: <original_ref_ID> <new_ref_ID>.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--seq_info"
alternatives:
- "-s"
description: "<seq_info.fsize> is a tab-delimited file providing this info for\
\ each of the mapped \nsequences: <seq-name> <seq-length> <seq-description>\
\ (useful for --description option with \nmRNA/EST/protein mappings).\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome"
alternatives:
- "-g"
description: "Full path to a multi-fasta file with the genomic sequences for all\
\ input mappings, \nOR a directory with single-fasta files (one per genomic\
\ sequence, with file names \nmatching sequence names).\n"
info: null
example:
- "genome.fa"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--outfile"
alternatives:
- "-o"
description: "Write the output records into <outfile>.\n"
info: null
example:
- "output.gff"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--force_exons"
description: "Make sure that the lowest level GFF features are considered \"exon\"\
\ features.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--gene2exon"
description: "For single-line genes not parenting any transcripts, add an exon\
\ feature spanning \nthe entire gene (treat it as a transcript).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--t_adopt"
description: "Try to find a parent gene overlapping/containing a transcript that\
\ does not have \nany explicit gene Parent.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--decode"
alternatives:
- "-D"
description: "Decode url encoded characters within attributes.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--merge_exons"
alternatives:
- "-Z"
description: "Merge very close exons into a single exon (when intron size<4).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--junctions"
alternatives:
- "-j"
description: "Output the junctions and the corresponding transcripts.\n"
info: null
direction: "input"
- type: "file"
name: "--spliced_exons"
alternatives:
- "-w"
description: "Write a fasta file with spliced exons for each transcript.\n"
info: null
example:
- "exons.fa"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--w_add"
description: "For the --spliced_exons option, extract additional <N> bases both\
\ upstream and \ndownstream of the transcript boundaries.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--w_nocds"
description: "For --spliced_exons, disable the output of CDS info in the FASTA\
\ file.\n"
info: null
direction: "input"
- type: "file"
name: "--spliced_cds"
alternatives:
- "-x"
description: "Write a fasta file with spliced CDS for each GFF transcript.\n"
info: null
example:
- "cds.fa"
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tr_cds"
alternatives:
- "-y"
description: "Write a protein fasta file with the translation of CDS for each\
\ record.\n"
info: null
example:
- "tr_cds.fa"
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--w_coords"
alternatives:
- "-W"
description: "For --spliced_exons, --spliced_cds and -tr_cds options, write in\
\ the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--stop_dot"
alternatives:
- "-S"
description: "For --tr_cds option, use '*' instead of '.' as stop codon translation.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--id_version"
alternatives:
- "-L"
description: "Ensembl GTF to GFF3 conversion, adds version to IDs.\n"
info: null
direction: "input"
- type: "string"
name: "--trackname"
alternatives:
- "-t"
description: "Use <trackname> in the 2nd column of each GFF/GTF output line.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--gtf_output"
alternatives:
- "-T"
description: "Main output will be GTF instead of GFF3.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--bed"
description: "Output records in BED format instead of default GFF3.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--tlf"
description: "Output \"transcript line format\" which is like GFF but with exons\
\ and CDS related \nfeatures stored as GFF attributes in the transcript feature\
\ line, like this:\n exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>\n\
<exons> is a comma-delimited list of exon_start-exon_end coordinates;\n<CDScoords>\
\ is CDS_start:CDS_end coordinates or a list like <exons>.\n"
info: null
direction: "input"
- type: "string"
name: "--table"
description: "Output a simple tab delimited format instead of GFF, with columns\
\ having the values \nof GFF attributes given in <attrlist>; special pseudo-attributes\
\ (prefixed by @) are \nrecognized:\n @id, @geneid, @chr, @start, @end, @strand,\
\ @numexons, @exons, @cds, @covlen, @cdslen\nIf any of --spliced_exons/--tr_cds/--spliced_cds\
\ FASTA output files are enabled, the \nsame fields (excluding @id) are appended\
\ to the definition line of corresponding FASTA\nrecords.\n"
info: null
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "boolean_true"
name: "--expose_dups"
alternatives:
- "-E"
- "-v"
description: "Expose (warn about) duplicate transcript IDs and other potential\
\ problems with the \ngiven GFF/GTF records.\n"
info: null
direction: "input"
- name: "Options"
arguments:
- type: "file"
name: "--ids"
description: "Discard records/transcripts if their IDs are not listed in <IDs.lst>.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--nids"
description: "Discard records/transcripts if their IDs are listed in <IDs.lst>.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--maxintron"
alternatives:
- "-i"
description: "Discard transcripts having an intron larger than <maxintron>.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--minlen"
alternatives:
- "-l"
description: "Discard transcripts shorter than <minlen> bases.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--range"
alternatives:
- "-r"
description: "Only show transcripts overlapping coordinate range <start>..<end>\
\ (on chromosome/contig \n<chr>, strand <strand> if provided).\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--strict_range"
alternatives:
- "-R"
description: "For --range option, discard all transcripts that are not fully contained\
\ within the given \nrange.\n"
info: null
direction: "input"
- type: "string"
name: "--jmatch"
description: "Only output transcripts matching the given junction.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--no_single_exon"
alternatives:
- "-U"
description: "Discard single-exon transcripts.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--coding"
alternatives:
- "-C"
description: "Coding only: discard mRNAs that have no CDS features.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--nc"
description: "Non-coding only: discard mRNAs that have CDS features.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--ignore_locus"
description: "Discard locus features and attributes found in the input.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--description"
alternatives:
- "-A"
description: "Use the description field from <seq_info.fsize> and add it as the\
\ value for a 'descr' \nattribute to the GFF record.\n"
info: null
direction: "input"
- name: "Sorting"
arguments:
- type: "boolean_true"
name: "--sort_alpha"
description: "Chromosomes (reference sequences) are sorted alphabetically.\n"
info: null
direction: "input"
- type: "file"
name: "--sort_by"
description: "Sort the reference sequences by the order in which their names are\
\ given in the \n<refseq.lst> file.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Misc options"
arguments:
- type: "boolean_true"
name: "--keep_attrs"
alternatives:
- "-F"
description: "Keep all GFF attributes (for non-exon features).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--keep_exon_attrs"
description: "For -F option, do not attempt to reduce redundant exon/CDS attributes.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_exon_attrs"
alternatives:
- "-G"
description: "Do not keep exon attributes, move them to the transcript feature\
\ (for GFF3 output).\n"
info: null
direction: "input"
- type: "string"
name: "--attrs"
description: "Only output the GTF/GFF attributes listed in <attr-list> which is\
\ a comma delimited \nlist of attribute names to.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--keep_genes"
description: "In transcript-only mode (default), also preserve gene records.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--keep_comments"
description: "For GFF3 input/output, try to preserve comments.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--process_other"
alternatives:
- "-O"
description: "process other non-transcript GFF records (by default non-transcript\
\ records are ignored).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--rm_stop_codons"
alternatives:
- "-V"
description: "Discard any mRNAs with CDS having in-frame stop codons (requires\
\ --genome).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--adj_cds_start"
alternatives:
- "-H"
description: "For --rm_stop_codons option, check and adjust the starting CDS phase\
\ if the original phase\nleads to a translation with an in-frame stop codon.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--opposite_strand"
alternatives:
- "-B"
description: "For -V option, single-exon transcripts are also checked on the opposite\
\ strand (requires \n--genome). \n"
info: null
direction: "input"
- type: "boolean_true"
name: "--coding_status"
alternatives:
- "-P"
description: "Add transcript level GFF attributes about the coding status of each\
\ transcript, including \npartialness or in-frame stop codons (requires --genome).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--add_hasCDS"
description: "Add a \"hasCDS\" attribute with value \"true\" for transcripts that\
\ have CDS features. \n"
info: null
direction: "input"
- type: "boolean_true"
name: "--adj_stop"
description: "Stop codon adjustment: enables --coding_status and performs automatic\
\ adjustment of the CDS stop \ncoordinate if premature or downstream.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--rm_noncanon"
alternatives:
- "-N"
description: "Discard multi-exon mRNAs that have any intron with a non-canonical\
\ splice site consensus \n(i.e. not GT-AG, GC-AG or AT-AC).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--complete_cds"
alternatives:
- "-J"
description: "Discard any mRNAs that either lack initial START codon or the terminal\
\ STOP codon, or \nhave an in-frame stop codon (i.e. only print mRNAs with a\
\ complete CDS).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_pseudo"
description: "Filter out records matching the 'pseudo' keyword.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--in_bed"
description: "Input should be parsed as BED format (automatic if the input filename\
\ ends with .bed*).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--in_tlf"
description: "Input GFF-like one-line-per-transcript format without exon/CDS features\
\ (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--stream"
description: "Fast processing of input GFF/BED transcripts as they are received\
\ (no sorting, exons must \nbe grouped by transcript in the input data).\n"
info: null
direction: "input"
- name: "Clustering"
arguments:
- type: "boolean_true"
name: "--merge"
alternatives:
- "-M"
description: "Cluster the input transcripts into loci, discarding \"redundant\"\
\ transcripts (those with \nthe same exact introns and fully contained or equal\
\ boundaries).\n"
info: null
direction: "input"
- type: "file"
name: "--dupinfo"
alternatives:
- "-d"
description: "For --merge option, write duplication info to file <dupinfo>.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--cluster_only"
description: "Same as --merge but without discarding any of the \"duplicate\"\
\ transcripts, only create \n\"locus\" features.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--rm_redundant"
alternatives:
- "-K"
description: "For --merge option: also discard as redundant the shorter, fully\
\ contained transcripts (intron \nchains matching a part of the container).\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_boundary"
alternatives:
- "-Q"
description: "For --merge option, no longer require boundary containment when\
\ assessing redundancy (can be \ncombined with --rm_redundant); only introns\
\ have to match for multi-exon transcripts, and >=80%\noverlap for single-exon\
\ transcripts.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_overlap"
alternatives:
- "-Y"
description: "For --merge option, enforce --no_boundary but also discard overlapping\
\ single-exon transcripts,\neven on the opposite strand (can be combined with\
\ --rm_redudant).\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Validate, filter, convert and perform various other operations on GFF\
\ 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:
- "gff"
- "conversion"
- "validation"
- "filtering"
license: "MIT"
references:
doi:
- "10.12688/f1000research.23297.2"
links:
repository: "https://github.com/gpertea/gffread"
homepage: "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread"
documentation: "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "echo \"gffread: \\\"$(gffread --version 2>&1)\\\"\" > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/gffread/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/gffread"
executable: "target/executable/gffread/gffread"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
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-RC7"
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"
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