Build branch qualimap with version qualimap (58d7dac)
Build pipeline: viash-hub.biobox.qualimap-nmgj2
Source commit: 58d7dacfc2
Source message: Update src/qualimap/qualimap_rnaseq/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
This commit is contained in:
170
target/executable/busco/busco_download_datasets/.config.vsh.yaml
Normal file
170
target/executable/busco/busco_download_datasets/.config.vsh.yaml
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@@ -0,0 +1,170 @@
|
||||
name: "busco_download_datasets"
|
||||
namespace: "busco"
|
||||
version: "qualimap"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--download"
|
||||
description: "Download dataset. Possible values are a specific dataset name, \"\
|
||||
all\", \"prokaryota\", \"eukaryota\", or \"virus\".\nThe full list of available\
|
||||
\ datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/)\
|
||||
\ or by running the busco/busco_list_datasets component.\n"
|
||||
info: null
|
||||
example:
|
||||
- "stramenopiles_odb10"
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--download_path"
|
||||
description: "Local filepath for storing BUSCO dataset downloads\n"
|
||||
info: null
|
||||
example:
|
||||
- "busco_downloads"
|
||||
default:
|
||||
- "busco_downloads"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Downloads available busco datasets"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "lineage datasets"
|
||||
license: "MIT"
|
||||
references:
|
||||
doi:
|
||||
- "10.1007/978-1-4939-9173-0_14"
|
||||
links:
|
||||
repository: "https://gitlab.com/ezlab/busco"
|
||||
homepage: "https://busco.ezlab.org/"
|
||||
documentation: "https://busco.ezlab.org/busco_userguide.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/busco:5.7.1--pyhdfd78af_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "qualimap"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/busco/busco_download_datasets/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/busco/busco_download_datasets"
|
||||
executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "58d7dacfc28af316aebc8f11c3facc6c9671e94b"
|
||||
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"
|
||||
1048
target/executable/busco/busco_download_datasets/busco_download_datasets
Executable file
1048
target/executable/busco/busco_download_datasets/busco_download_datasets
Executable file
File diff suppressed because it is too large
Load Diff
157
target/executable/busco/busco_list_datasets/.config.vsh.yaml
Normal file
157
target/executable/busco/busco_list_datasets/.config.vsh.yaml
Normal file
@@ -0,0 +1,157 @@
|
||||
name: "busco_list_datasets"
|
||||
namespace: "busco"
|
||||
version: "qualimap"
|
||||
argument_groups:
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output file of the available busco datasets\n"
|
||||
info: null
|
||||
example:
|
||||
- "file.txt"
|
||||
default:
|
||||
- "busco_dataset_list.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Lists the available busco datasets"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "lineage datasets"
|
||||
license: "MIT"
|
||||
references:
|
||||
doi:
|
||||
- "10.1007/978-1-4939-9173-0_14"
|
||||
links:
|
||||
repository: "https://gitlab.com/ezlab/busco"
|
||||
homepage: "https://busco.ezlab.org/"
|
||||
documentation: "https://busco.ezlab.org/busco_userguide.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/busco:5.7.1--pyhdfd78af_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "qualimap"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/busco/busco_list_datasets/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/busco/busco_list_datasets"
|
||||
executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "58d7dacfc28af316aebc8f11c3facc6c9671e94b"
|
||||
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"
|
||||
1020
target/executable/busco/busco_list_datasets/busco_list_datasets
Executable file
1020
target/executable/busco/busco_list_datasets/busco_list_datasets
Executable file
File diff suppressed because it is too large
Load Diff
435
target/executable/busco/busco_run/.config.vsh.yaml
Normal file
435
target/executable/busco/busco_run/.config.vsh.yaml
Normal file
@@ -0,0 +1,435 @@
|
||||
name: "busco_run"
|
||||
namespace: "busco"
|
||||
version: "qualimap"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input sequence file in FASTA format. Can be an assembled genome\
|
||||
\ or transcriptome (DNA), or protein sequences from an annotated gene set. Also\
|
||||
\ possible to use a path to a directory containing multiple input files.\n"
|
||||
info: null
|
||||
example:
|
||||
- "file.fasta"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--mode"
|
||||
alternatives:
|
||||
- "-m"
|
||||
description: "Specify which BUSCO analysis mode to run. There are three valid\
|
||||
\ modes:\n - geno or genome, for genome assemblies (DNA)\n - tran or transcriptome,\
|
||||
\ for transcriptome assemblies (DNA)\n - prot or proteins, for annotated gene\
|
||||
\ sets (protein)\n"
|
||||
info: null
|
||||
example:
|
||||
- "proteins"
|
||||
required: true
|
||||
choices:
|
||||
- "genome"
|
||||
- "geno"
|
||||
- "transcriptome"
|
||||
- "tran"
|
||||
- "proteins"
|
||||
- "prot"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--lineage_dataset"
|
||||
alternatives:
|
||||
- "-l"
|
||||
description: "Specify a BUSCO lineage dataset that is most closely related to\
|
||||
\ the assembly or gene set being assessed. \nThe full list of available datasets\
|
||||
\ can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by\
|
||||
\ running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\"\
|
||||
\ flag can be set to automatically find the optimal lineage path.\nBUSCO will\
|
||||
\ automatically download the requested dataset if it is not already present\
|
||||
\ in the download folder. \nYou can optionally provide a path to a local dataset\
|
||||
\ instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using\
|
||||
\ the busco/busco_download_dataset component.\n"
|
||||
info: null
|
||||
example:
|
||||
- "stramenopiles_odb10"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--short_summary_json"
|
||||
description: "Output file for short summary in JSON format.\n"
|
||||
info: null
|
||||
example:
|
||||
- "short_summary.json"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--short_summary_txt"
|
||||
description: "Output file for short summary in TXT format.\n"
|
||||
info: null
|
||||
example:
|
||||
- "short_summary.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--full_table"
|
||||
description: "Full table output in TSV format.\n"
|
||||
info: null
|
||||
example:
|
||||
- "full_table.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--missing_busco_list"
|
||||
description: "Missing list output in TSV format.\n"
|
||||
info: null
|
||||
example:
|
||||
- "missing_busco_list.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_dir"
|
||||
description: "The full output directory, if so desired.\n"
|
||||
info: null
|
||||
example:
|
||||
- "output_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Resource and Run Settings"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--force"
|
||||
description: "Force rewriting of existing files. Must be used when output files\
|
||||
\ with the provided name already exist.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--quiet"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Disable the info logs, displays only errors.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--restart"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "Continue a run that had already partially completed. Restarting\
|
||||
\ skips calls to tools that have completed but performs all pre- and post-processing\
|
||||
\ steps.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--tar"
|
||||
description: "Compress some subdirectories with many files to save space.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Lineage Dataset Settings"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--auto_lineage"
|
||||
description: "Run auto-lineage pipelilne to automatically determine BUSCO lineage\
|
||||
\ dataset that is most closely related to the assembly or gene set being assessed.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--auto_lineage_euk"
|
||||
description: "Run auto-placement just on eukaryota tree to find optimal lineage\
|
||||
\ path.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--auto_lineage_prok"
|
||||
description: "Run auto_lineage just on prokaryota trees to find optimum lineage\
|
||||
\ path.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--datasets_version"
|
||||
description: "Specify the version of BUSCO datasets\n"
|
||||
info: null
|
||||
example:
|
||||
- "odb10"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Augustus Settings"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--augustus"
|
||||
description: "Use augustus gene predictor for eukaryote runs.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--augustus_parameters"
|
||||
description: "Additional parameters to be passed to Augustus (see Augustus documentation:\
|
||||
\ https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\n\
|
||||
Parameters should be contained within a single string, without whitespace and\
|
||||
\ seperated by commas.\n"
|
||||
info: null
|
||||
example:
|
||||
- "--PARAM1=VALUE1,--PARAM2=VALUE2"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--augustus_species"
|
||||
description: "Specify the augustus species\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--long"
|
||||
description: "Optimize Augustus self-training mode. This adds considerably to\
|
||||
\ the run time, but can improve results for some non-model organisms.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "BBTools Settings"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--contig_break"
|
||||
description: "Number of contiguous Ns to signify a break between contigs in BBTools\
|
||||
\ analysis.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--limit"
|
||||
description: "Number of candidate regions (contig or transcript) from the BLAST\
|
||||
\ output to consider per BUSCO.\nThis option is only effective in pipelines\
|
||||
\ using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome\
|
||||
\ pipeline.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--scaffold_composition"
|
||||
description: "Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "BLAST Settings"
|
||||
arguments:
|
||||
- type: "double"
|
||||
name: "--e_value"
|
||||
description: "E-value cutoff for BLAST searches.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Protein Gene Prediction settings"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--miniprot"
|
||||
description: "Use Miniprot gene predictor.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "MetaEuk Settings"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--metaeuk"
|
||||
description: "Use Metaeuk gene predictor.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--metaeuk_parameters"
|
||||
description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\
|
||||
\ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
|
||||
\ be contained within a single string with no white space, with each parameter\
|
||||
\ separated by a comma.\n"
|
||||
info: null
|
||||
example:
|
||||
- "--max-overlap=15,--min-exon-aa=15"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--metaeuk_rerun_parameters"
|
||||
description: "Pass additional arguments to Metaeuk for the second run (see Metaeuk\
|
||||
\ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
|
||||
\ be contained within a single string with no white space, with each parameter\
|
||||
\ separated by a comma.\n"
|
||||
info: null
|
||||
example:
|
||||
- "--max-overlap=15,--min-exon-aa=15"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Assessment of genome assembly and annotation completeness with single\
|
||||
\ copy orthologs"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_data"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "Genome assembly"
|
||||
- "quality control"
|
||||
license: "MIT"
|
||||
references:
|
||||
doi:
|
||||
- "10.1007/978-1-4939-9173-0_14"
|
||||
links:
|
||||
repository: "https://gitlab.com/ezlab/busco"
|
||||
homepage: "https://busco.ezlab.org/"
|
||||
documentation: "https://busco.ezlab.org/busco_userguide.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/busco:5.7.1--pyhdfd78af_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "qualimap"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/busco/busco_run/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/busco/busco_run"
|
||||
executable: "target/executable/busco/busco_run/busco_run"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "58d7dacfc28af316aebc8f11c3facc6c9671e94b"
|
||||
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"
|
||||
1743
target/executable/busco/busco_run/busco_run
Executable file
1743
target/executable/busco/busco_run/busco_run
Executable file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user