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14e0d1218968fbb872b137c8bc45f204684a8b89
rnaseq/target/executable/qualimap/.config.vsh.yaml
CI 14e0d12189 Build branch main with version main (ce40a4a) 
Build pipeline: viash-hub.rnaseq.main-b6jtr

Source commit: ce40a4a6d9

Source message: add unit tests
2024-11-27 09:19:16 +00:00

302 lines
8.1 KiB
YAML
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name: "qualimap"
version: "main"
argument_groups:
- name: "Input"
arguments:
- type: "file"
name: "--input"
description: "path to input mapping file in BAM format."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gtf"
description: "path to annotations file in Ensembl GTF format."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--output_dir"
description: "path to output directory for raw data and report."
info: null
default:
- "$id.qualimap_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output_pdf"
description: "path to output file for pdf report."
info: null
default:
- "$id.report.pdf"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--output_format"
description: "Format of the output report (PDF or HTML, default is HTML)"
info: null
default:
- "html"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Optional"
arguments:
- type: "integer"
name: "--pr_bases"
description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
\ bias (default = 100)."
info: null
default:
- 100
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--tr_bias"
description: "Number of top highly expressed transcripts to compute 5'-3' bias\
\ (default = 1000)."
info: null
default:
- 1000
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--algorithm"
description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
info: null
default:
- "uniquely-mapped-reads"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--sequencing_protocol"
description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
\ or non-strand-specific (default))."
info: null
default:
- "non-strand-specific"
required: false
choices:
- "non-strand-specific"
- "strand-specific-reverse"
- "strand-specific-forward"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--paired"
description: "Setting this flag for paired-end experiments will result in counting\
\ fragments instead of reads."
info: null
direction: "input"
- type: "boolean_true"
name: "--sorted"
description: "Setting this flag indicates that the input file is already sorted\
\ by name. If flag is not set, additional sorting by name will be performed.\
\ Only requiredfor paired-end analysis."
info: null
direction: "input"
- type: "string"
name: "--java_memory_size"
description: "maximum Java heap memory size, default = 4G."
info: null
default:
- "4G"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "RNA-seq QC analysis using the qualimap \n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam"
- type: "file"
path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai"
- type: "file"
path: "genes.gtf"
info:
migration_info:
git_repo: "https://github.com/nf-core/rnaseq.git"
paths:
- "modules/nf-core/qualimap/rnaseq/main.nf"
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
status: "enabled"
requirements:
commands:
- "ps"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
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:
- "r-base"
- "unzip"
- "wget"
- "openjdk-8-jdk"
- "libxml2-dev"
- "libcurl4-openssl-dev"
interactive: false
- type: "docker"
run:
- "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip &&\
\ \\\nunzip qualimap_v2.3.zip && \\\ncp -a qualimap_v2.3/. usr/bin && \\\nunset\
\ DISPLAY && \\\nmkdir -p tmp && \\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp\n"
- type: "r"
cran:
- "optparse"
bioc:
- "NOISeqr"
bioc_force_install: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/qualimap/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
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"
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