Build branch main with version main (1e1ffb3)
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
This commit is contained in:
174
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
Normal file
174
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
Normal file
@@ -0,0 +1,174 @@
|
||||
name: "rseqc_bamstat"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
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: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "output file (txt) with mapping quality statistics"
|
||||
info: null
|
||||
default:
|
||||
- "$id.mapping_quality.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Generate statistics from a bam file.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/bamstat/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1118
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
Executable file
1118
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
Executable file
File diff suppressed because it is too large
Load Diff
197
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
Normal file
197
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
Normal file
@@ -0,0 +1,197 @@
|
||||
name: "rseqc_inferexperiment"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
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"
|
||||
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"
|
||||
description: "Numer of reads sampled from SAM/BAM file, default = 200000."
|
||||
info: null
|
||||
default:
|
||||
- 200000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "output file (txt) of strandness report"
|
||||
info: null
|
||||
default:
|
||||
- "$id.strandedness.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: "Infer strandedness from sequencing reads\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/inferexperiment/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1182
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
Executable file
1182
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
Executable file
File diff suppressed because it is too large
Load Diff
283
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
Normal file
283
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
Normal file
@@ -0,0 +1,283 @@
|
||||
name: "rseqc_innerdistance"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
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"
|
||||
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"
|
||||
description: "Numer of reads sampled from SAM/BAM file, default = 200000."
|
||||
info: null
|
||||
default:
|
||||
- 200000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--lower_bound_size"
|
||||
description: "Lower bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=-250."
|
||||
info: null
|
||||
default:
|
||||
- -250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--upper_bound_size"
|
||||
description: "Upper bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=250."
|
||||
info: null
|
||||
default:
|
||||
- 250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--step_size"
|
||||
description: "Step size (bp) of histograme. This option is used for plotting histogram,\
|
||||
\ default=5."
|
||||
info: null
|
||||
default:
|
||||
- 5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_stats"
|
||||
description: "output file (txt) with summary statistics of inner distances of\
|
||||
\ paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance.stats"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_dist"
|
||||
description: "output file (txt) with inner distances of all paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance.txt"
|
||||
must_exist: false
|
||||
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
|
||||
default:
|
||||
- "$id.inner_distance_freq.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot"
|
||||
description: "output file (pdf) with histogram plot of of inner distances of all\
|
||||
\ paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance_plot.pdf"
|
||||
must_exist: false
|
||||
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
|
||||
default:
|
||||
- "$id.inner_distance_plot.r"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate inner distance between read pairs. \n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/innerdistance/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_innerdistance/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_innerdistance"
|
||||
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1397
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
Executable file
1397
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
Executable file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,271 @@
|
||||
name: "rseqc_junctionannotation"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
description: "Reference gene model in bed format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_intron"
|
||||
description: "Minimum intron length (bp), default = 50."
|
||||
info: null
|
||||
default:
|
||||
- 50
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_log"
|
||||
description: "output log of junction annotation script"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_annotation.log"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot_r"
|
||||
description: "r script to generate splice_junction and splice_events plot"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_annotation_plot.r"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_junction_bed"
|
||||
description: "junction annotation file (bed format)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_annotation.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_junction_interact"
|
||||
description: "interact file (bed format) of junctions. Can be uploaded to UCSC\
|
||||
\ genome browser or converted to bigInteract (using bedToBigBed program) for\
|
||||
\ visualization."
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_annotation.Interact.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_junction_sheet"
|
||||
description: "junction annotation file (xls format)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_annotation.xls"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_splice_events_plot"
|
||||
description: "plot of splice events (pdf)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.splice_events.pdf"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_splice_junctions_plot"
|
||||
description: "plot of junctions (pdf)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.splice_junctions_plot.pdf"
|
||||
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: "Compare detected splice junctions to reference gene model.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/junctionannotation/main.nf"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_junctionannotation/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_junctionannotation"
|
||||
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1404
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
Executable file
1404
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
Executable file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,260 @@
|
||||
name: "rseqc_junctionsaturation"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
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"
|
||||
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: "--sampling_percentile_lower_bound"
|
||||
description: "Sampling starts from this percentile, must be an integer between\
|
||||
\ 0 and 100, default =5."
|
||||
info: null
|
||||
default:
|
||||
- 5
|
||||
required: false
|
||||
min: 0
|
||||
max: 100
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sampling_percentile_upper_bound"
|
||||
description: "Sampling ends at this percentile, must be an integer between 0 and\
|
||||
\ 100, default =5."
|
||||
info: null
|
||||
default:
|
||||
- 100
|
||||
required: false
|
||||
min: 0
|
||||
max: 100
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sampling_percentile_step"
|
||||
description: "Sampling frequency in %. Smaller value means more sampling times.\
|
||||
\ Must be an integer between 0 and 100, default = 5."
|
||||
info: null
|
||||
default:
|
||||
- 5
|
||||
required: false
|
||||
min: 0
|
||||
max: 100
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_intron"
|
||||
description: "Minimum intron length (bp), default = 50."
|
||||
info: null
|
||||
default:
|
||||
- 50
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_splice_read"
|
||||
description: "Minimum number of supporting reads to call a junction, default =\
|
||||
\ 1."
|
||||
info: null
|
||||
default:
|
||||
- 1
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_plot_r"
|
||||
description: "r script to generate junction_saturation_plot plot"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_saturation_plot.r"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot"
|
||||
description: "plot of junction saturation (pdf)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.junction_saturation_plot.pdf"
|
||||
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: "Compare detected splice junctions to reference gene model.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/junctionsaturation/main.nf"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_junctionsaturation/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_junctionsaturation"
|
||||
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1368
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
Executable file
1368
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
Executable file
File diff suppressed because it is too large
Load Diff
173
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
Normal file
173
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
Normal file
@@ -0,0 +1,173 @@
|
||||
name: "rseqc_readdistribution"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
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"
|
||||
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 read distribution analysis."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_distribution.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate how mapped reads are distributed over genomic features.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/readdistribution/main.nf"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_readdistribution/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_readdistribution"
|
||||
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1117
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
Executable file
1117
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
Executable file
File diff suppressed because it is too large
Load Diff
222
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
Normal file
222
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
Normal file
@@ -0,0 +1,222 @@
|
||||
name: "rseqc_readduplication"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--read_count_upper_limit"
|
||||
description: "Upper limit of reads' occurence. Only used for plotting, default\
|
||||
\ = 500 (times)."
|
||||
info: null
|
||||
default:
|
||||
- 500
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_duplication_rate_plot_r"
|
||||
description: "R script for generating duplication rate plot"
|
||||
info: null
|
||||
default:
|
||||
- "$id.duplication_rate_plot.r"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_duplication_rate_plot"
|
||||
description: "duplication rate plot (pdf)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.duplication_rate_plot.pdf"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_duplication_rate_mapping"
|
||||
description: "Summary of mapping-based read duplication"
|
||||
info: null
|
||||
default:
|
||||
- "$id.duplication_rate_mapping.xls"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_duplication_rate_sequence"
|
||||
description: "Summary of sequencing-based read duplication"
|
||||
info: null
|
||||
default:
|
||||
- "$id.duplication_rate_sequencing.xls"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate read duplication rate.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/readduplication/main.nf"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_readduplication/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_readduplication"
|
||||
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1263
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
Executable file
1263
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
Executable file
File diff suppressed because it is too large
Load Diff
225
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
Normal file
225
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
Normal file
@@ -0,0 +1,225 @@
|
||||
name: "rseqc_tin"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--bam_input"
|
||||
description: "Path to 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: "--bai_input"
|
||||
description: "Path to bam index file in bai format."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
description: "BED file containing the reference gene model"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--minimum_coverage"
|
||||
description: "Minimum number of reads mapped to a transcript, default = 10."
|
||||
info: null
|
||||
default:
|
||||
- 10
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sample_size"
|
||||
description: "Number of equal-spaced nucleotide positions picked from mRNA. Note,\
|
||||
\ if this number is larger than the length of mRNA (L), it will be halved until\
|
||||
\ it's smaller than L (default = 100)"
|
||||
info: null
|
||||
default:
|
||||
- 100
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--subtract_background"
|
||||
description: "Set flag to subtract background noise (estimated from intronic reads).\
|
||||
\ Only use this option if there are substantial intronic reads."
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_tin_summary"
|
||||
description: "summary statistics (txt) of calculated TIN metrics"
|
||||
info: null
|
||||
default:
|
||||
- "$id.tin_summary.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_tin"
|
||||
description: "file with TIN metrics (xls)"
|
||||
info: null
|
||||
default:
|
||||
- "$id.tin.xls"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculte TIN (transcript integrity number) from RNA-seq reads\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam.bai"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/tin/main.nf"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "pip3 install RSeQC\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/tin/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_tin"
|
||||
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
|
||||
git_remote: "https://github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
1287
target/executable/rseqc/rseqc_tin/rseqc_tin
Executable file
1287
target/executable/rseqc/rseqc_tin/rseqc_tin
Executable file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user