Build branch main with version main (aa43543)
Build pipeline: viash-hub.biobox.main-2k68h
Source commit: aa43543e1f
Source message: Rseqc innerdistance (#159)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* full component with two tests
* fix default values
* adjust argument names and container image
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
This commit is contained in:
202
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
Normal file
202
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
Normal file
@@ -0,0 +1,202 @@
|
||||
name: "rseqc_bamstat"
|
||||
namespace: "rseqc"
|
||||
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: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_file"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input alignment file in BAM or SAM format."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--mapq"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads. Default: '30'.\n"
|
||||
info: null
|
||||
example:
|
||||
- 30
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output file (txt) with mapping quality statistics."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Generate statistics from a bam file."
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_data"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "rnaseq"
|
||||
- "genomics"
|
||||
license: "GPL-3.0"
|
||||
references:
|
||||
doi:
|
||||
- "10.1093/bioinformatics/bts356"
|
||||
links:
|
||||
repository: "https://github.com/MonashBioinformaticsPlatform/RSeQC"
|
||||
homepage: "https://rseqc.sourceforge.net/"
|
||||
documentation: "https://rseqc.sourceforge.net/#bam-stat-py"
|
||||
issue_tracker: "https://github.com/MonashBioinformaticsPlatform/RSeQC/issues"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)\" > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_bamstat/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_bamstat"
|
||||
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
|
||||
git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
|
||||
git_tag: "v0.2.0-20-gaa43543"
|
||||
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"
|
||||
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"
|
||||
1119
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
Executable file
1119
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
Executable file
File diff suppressed because it is too large
Load Diff
228
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
Normal file
228
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
Normal file
@@ -0,0 +1,228 @@
|
||||
name: "rseqc_inferexperiment"
|
||||
namespace: "rseqc"
|
||||
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: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_file"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "Reference gene model in bed format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output file (txt) of strandness report."
|
||||
info: null
|
||||
example:
|
||||
- "$id.strandedness.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Options"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--sample_size"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Number of reads sampled from SAM/BAM file. Default: 200000\n"
|
||||
info: null
|
||||
example:
|
||||
- 200000
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--mapq"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads. Default: 30\n"
|
||||
info: null
|
||||
example:
|
||||
- 30
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Infer strandedness from sequencing reads\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_data"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "GPL-3.0"
|
||||
references:
|
||||
doi:
|
||||
- "10.1093/bioinformatics/bts356"
|
||||
links:
|
||||
repository: "https://github.com/MonashBioinformaticsPlatform/RSeQC"
|
||||
homepage: "https://rseqc.sourceforge.net/"
|
||||
documentation: "https://rseqc.sourceforge.net/#infer-experiment-py"
|
||||
issue_tracker: "https://github.com/MonashBioinformaticsPlatform/RSeQC/issues"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d'\
|
||||
\ ' -f2)\" > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_inferexperiment/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_inferexperiment"
|
||||
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
|
||||
git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
|
||||
git_tag: "v0.2.0-20-gaa43543"
|
||||
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"
|
||||
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"
|
||||
1192
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
Executable file
1192
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
Executable file
File diff suppressed because it is too large
Load Diff
321
target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml
Normal file
321
target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml
Normal file
@@ -0,0 +1,321 @@
|
||||
name: "rseqc_inner_distance"
|
||||
namespace: "rseqc"
|
||||
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: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_file"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "Reference gene model in bed format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sample_size"
|
||||
alternatives:
|
||||
- "-k"
|
||||
description: "Numer of reads sampled from SAM/BAM file, default = 1000000."
|
||||
info: null
|
||||
example:
|
||||
- 1000000
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--mapq"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
example:
|
||||
- 30
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--lower_bound"
|
||||
alternatives:
|
||||
- "-l"
|
||||
description: "Lower bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=-250."
|
||||
info: null
|
||||
example:
|
||||
- -250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--upper_bound"
|
||||
alternatives:
|
||||
- "-u"
|
||||
description: "Upper bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=250."
|
||||
info: null
|
||||
example:
|
||||
- 250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--step"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Step size (bp) of histograme. This option is used for plotting histogram,\
|
||||
\ default=5."
|
||||
info: null
|
||||
example:
|
||||
- 5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--output_prefix"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Rrefix of output files."
|
||||
info: null
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_stats"
|
||||
description: "output file (txt) with summary statistics of inner distances of\
|
||||
\ paired reads"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_dist"
|
||||
description: "output file (txt) with inner distances of all paired reads"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_freq"
|
||||
description: "output file (txt) with frequencies of inner distances of all paired\
|
||||
\ reads"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot"
|
||||
description: "output file (pdf) with histogram plot of of inner distances of all\
|
||||
\ paired reads"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot_r"
|
||||
description: "output file (R) with script of histogram plot of of inner distances\
|
||||
\ of all paired reads"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate inner distance between read pairs.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_data"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "GPL-3.0"
|
||||
references:
|
||||
doi:
|
||||
- "10.1093/bioinformatics/bts356"
|
||||
links:
|
||||
repository: "https://github.com/MonashBioinformaticsPlatform/RSeQC"
|
||||
homepage: "https://rseqc.sourceforge.net/"
|
||||
documentation: "https://rseqc.sourceforge.net/#inner-distance-py"
|
||||
issue_tracker: "https://github.com/MonashBioinformaticsPlatform/RSeQC/issues"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' '\
|
||||
\ -f2)\" > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_inner_distance/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_inner_distance"
|
||||
executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
|
||||
git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
|
||||
git_tag: "v0.2.0-20-gaa43543"
|
||||
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"
|
||||
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"
|
||||
1449
target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
Executable file
1449
target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
Executable file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user