Build branch v0.1 with version v0.1 (373be82)
Build pipeline: viash-hub.craftbox.v0.1-4f4mc
Source commit: 373be82129
Source message: Bump viash to 0.9.0-RC7 (#6)
This commit is contained in:
197
target/nextflow/concat_text/.config.vsh.yaml
Normal file
197
target/nextflow/concat_text/.config.vsh.yaml
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@@ -0,0 +1,197 @@
|
||||
name: "concat_text"
|
||||
version: "v0.1"
|
||||
authors:
|
||||
- name: "Toni Verbeiren"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
links:
|
||||
github: "tverbeiren"
|
||||
linkedin: "verbeiren"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist and CEO"
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "reviewer"
|
||||
info:
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "A list of (gzipped) text files."
|
||||
info: null
|
||||
example:
|
||||
- "input?.txt.gz"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--gzip_output"
|
||||
description: "Should the output be zipped?"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "File to write the output to, optionally gzipped."
|
||||
info: null
|
||||
example:
|
||||
- "output.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: "Concatenate a number of text files, handle gzipped text files gracefully\
|
||||
\ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
|
||||
\ fastq files from different lanes, for instance.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info:
|
||||
improvements: "This component could be improved in 2 ways:\n 1. Allow for a mix\
|
||||
\ of zipped and plain input files\n 2. Allow to specify a compression algorithm\
|
||||
\ for the output\n"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
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: "alpine:latest"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.1"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apk"
|
||||
packages:
|
||||
- "bash"
|
||||
- "procps"
|
||||
- "file"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/concat_text/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/concat_text"
|
||||
executable: "target/nextflow/concat_text/main.nf"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "v0.1"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
|
||||
keywords:
|
||||
- "scripts"
|
||||
- "custom"
|
||||
- "implementations"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
issue_tracker: "https://github.com/viash-hub/craftbox/issues"
|
||||
3602
target/nextflow/concat_text/main.nf
Normal file
3602
target/nextflow/concat_text/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
126
target/nextflow/concat_text/nextflow.config
Normal file
126
target/nextflow/concat_text/nextflow.config
Normal file
@@ -0,0 +1,126 @@
|
||||
manifest {
|
||||
name = 'concat_text'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.1'
|
||||
description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
|
||||
author = 'Toni Verbeiren, Dries Schaumont'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
// detect tempdir
|
||||
tempDir = java.nio.file.Paths.get(
|
||||
System.getenv('NXF_TEMP') ?:
|
||||
System.getenv('VIASH_TEMP') ?:
|
||||
System.getenv('TEMPDIR') ?:
|
||||
System.getenv('TMPDIR') ?:
|
||||
'/tmp'
|
||||
).toAbsolutePath()
|
||||
|
||||
profiles {
|
||||
no_publish {
|
||||
process {
|
||||
withName: '.*' {
|
||||
publishDir = [
|
||||
enabled: false
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
mount_temp {
|
||||
docker.temp = tempDir
|
||||
podman.temp = tempDir
|
||||
charliecloud.temp = tempDir
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
// docker.userEmulation = true
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
docker.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
podman {
|
||||
podman.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
shifter {
|
||||
shifter.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
charliecloud {
|
||||
charliecloud.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
}
|
||||
}
|
||||
|
||||
process{
|
||||
withLabel: mem1gb { memory = 1000000000.B }
|
||||
withLabel: mem2gb { memory = 2000000000.B }
|
||||
withLabel: mem5gb { memory = 5000000000.B }
|
||||
withLabel: mem10gb { memory = 10000000000.B }
|
||||
withLabel: mem20gb { memory = 20000000000.B }
|
||||
withLabel: mem50gb { memory = 50000000000.B }
|
||||
withLabel: mem100gb { memory = 100000000000.B }
|
||||
withLabel: mem200gb { memory = 200000000000.B }
|
||||
withLabel: mem500gb { memory = 500000000000.B }
|
||||
withLabel: mem1tb { memory = 1000000000000.B }
|
||||
withLabel: mem2tb { memory = 2000000000000.B }
|
||||
withLabel: mem5tb { memory = 5000000000000.B }
|
||||
withLabel: mem10tb { memory = 10000000000000.B }
|
||||
withLabel: mem20tb { memory = 20000000000000.B }
|
||||
withLabel: mem50tb { memory = 50000000000000.B }
|
||||
withLabel: mem100tb { memory = 100000000000000.B }
|
||||
withLabel: mem200tb { memory = 200000000000000.B }
|
||||
withLabel: mem500tb { memory = 500000000000000.B }
|
||||
withLabel: mem1gib { memory = 1073741824.B }
|
||||
withLabel: mem2gib { memory = 2147483648.B }
|
||||
withLabel: mem4gib { memory = 4294967296.B }
|
||||
withLabel: mem8gib { memory = 8589934592.B }
|
||||
withLabel: mem16gib { memory = 17179869184.B }
|
||||
withLabel: mem32gib { memory = 34359738368.B }
|
||||
withLabel: mem64gib { memory = 68719476736.B }
|
||||
withLabel: mem128gib { memory = 137438953472.B }
|
||||
withLabel: mem256gib { memory = 274877906944.B }
|
||||
withLabel: mem512gib { memory = 549755813888.B }
|
||||
withLabel: mem1tib { memory = 1099511627776.B }
|
||||
withLabel: mem2tib { memory = 2199023255552.B }
|
||||
withLabel: mem4tib { memory = 4398046511104.B }
|
||||
withLabel: mem8tib { memory = 8796093022208.B }
|
||||
withLabel: mem16tib { memory = 17592186044416.B }
|
||||
withLabel: mem32tib { memory = 35184372088832.B }
|
||||
withLabel: mem64tib { memory = 70368744177664.B }
|
||||
withLabel: mem128tib { memory = 140737488355328.B }
|
||||
withLabel: mem256tib { memory = 281474976710656.B }
|
||||
withLabel: mem512tib { memory = 562949953421312.B }
|
||||
withLabel: cpu1 { cpus = 1 }
|
||||
withLabel: cpu2 { cpus = 2 }
|
||||
withLabel: cpu5 { cpus = 5 }
|
||||
withLabel: cpu10 { cpus = 10 }
|
||||
withLabel: cpu20 { cpus = 20 }
|
||||
withLabel: cpu50 { cpus = 50 }
|
||||
withLabel: cpu100 { cpus = 100 }
|
||||
withLabel: cpu200 { cpus = 200 }
|
||||
withLabel: cpu500 { cpus = 500 }
|
||||
withLabel: cpu1000 { cpus = 1000 }
|
||||
}
|
||||
|
||||
|
||||
106
target/nextflow/concat_text/nextflow_schema.json
Normal file
106
target/nextflow/concat_text/nextflow_schema.json
Normal file
@@ -0,0 +1,106 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "concat_text",
|
||||
"description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files",
|
||||
"help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"output arguments" : {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"gzip_output": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Should the output be zipped?"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped."
|
||||
,
|
||||
"default": "$id.$key.output.txt"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"param_list": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
||||
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
||||
"hidden": true
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/input arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/output arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
248
target/nextflow/csv2fasta/.config.vsh.yaml
Normal file
248
target/nextflow/csv2fasta/.config.vsh.yaml
Normal file
@@ -0,0 +1,248 @@
|
||||
name: "csv2fasta"
|
||||
version: "v0.1"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "CSV file to be processed."
|
||||
info: null
|
||||
example:
|
||||
- "barcodes.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--header"
|
||||
description: "Parse the first line of the CSV file as a header.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "CSV dialect options"
|
||||
description: "Options that can be used to override the automatically detected\n\
|
||||
dialect of the CSV file.\n"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--delimiter"
|
||||
description: "Overwrite the column delimiter character.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--quote_character"
|
||||
description: "Overwrite the character used to denote the start and end of a quoted\
|
||||
\ item.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "CSV column arguments"
|
||||
description: "Parameters for the selection of columns from the CSV file.\nOnly required\
|
||||
\ when your CSV file contains more than 2 columns,\notherwise the first column\
|
||||
\ will be used for the FASTA header\nand the second for the FASTA nucleotide sequences.\
|
||||
\ This default\ncan still be overwritten by using the options below.\n"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--sequence_column"
|
||||
description: "Name of the column containing the sequences. Implies 'header'.\n\
|
||||
Cannot be used together with 'sequence_column_index'.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--name_column"
|
||||
description: "Name of the column describing the FASTA headers. Implies 'header'.\n\
|
||||
Cannot be used together with 'name_column_index'.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sequence_column_index"
|
||||
description: "Index of the column to use as the FASTA sequences, counter from\
|
||||
\ the left and\nstarting from 0. Cannot be used in combination with the 'sequence_column'\
|
||||
\ argument.\n"
|
||||
info: null
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--name_column_index"
|
||||
description: "Index of the column to use as the FASTA headers, counter from the\
|
||||
\ left and\nstarting from 0. Cannot be used in combination with 'name_column'.\n"
|
||||
info: null
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output fasta file."
|
||||
info: null
|
||||
example:
|
||||
- "barcodes.fasta"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
|
||||
contain an optional header and each row (other than the header) becomes\na single\
|
||||
\ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
|
||||
\ entries, while the other become the sequences. The sequences\ncolumn must only\
|
||||
\ contain characters that are valid IUPAC notation for \nnucleotides or a group\
|
||||
\ thereof (wildcard characters).\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test_csv2fasta.py"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
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:slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.1"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "dnaio"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "pytest"
|
||||
- "viashpy"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/csv2fasta/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/csv2fasta"
|
||||
executable: "target/nextflow/csv2fasta/main.nf"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "v0.1"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
|
||||
keywords:
|
||||
- "scripts"
|
||||
- "custom"
|
||||
- "implementations"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
issue_tracker: "https://github.com/viash-hub/craftbox/issues"
|
||||
3714
target/nextflow/csv2fasta/main.nf
Normal file
3714
target/nextflow/csv2fasta/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
125
target/nextflow/csv2fasta/nextflow.config
Normal file
125
target/nextflow/csv2fasta/nextflow.config
Normal file
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'csv2fasta'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.1'
|
||||
description = 'Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
// detect tempdir
|
||||
tempDir = java.nio.file.Paths.get(
|
||||
System.getenv('NXF_TEMP') ?:
|
||||
System.getenv('VIASH_TEMP') ?:
|
||||
System.getenv('TEMPDIR') ?:
|
||||
System.getenv('TMPDIR') ?:
|
||||
'/tmp'
|
||||
).toAbsolutePath()
|
||||
|
||||
profiles {
|
||||
no_publish {
|
||||
process {
|
||||
withName: '.*' {
|
||||
publishDir = [
|
||||
enabled: false
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
mount_temp {
|
||||
docker.temp = tempDir
|
||||
podman.temp = tempDir
|
||||
charliecloud.temp = tempDir
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
// docker.userEmulation = true
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
docker.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
podman {
|
||||
podman.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
shifter {
|
||||
shifter.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
charliecloud {
|
||||
charliecloud.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
}
|
||||
}
|
||||
|
||||
process{
|
||||
withLabel: mem1gb { memory = 1000000000.B }
|
||||
withLabel: mem2gb { memory = 2000000000.B }
|
||||
withLabel: mem5gb { memory = 5000000000.B }
|
||||
withLabel: mem10gb { memory = 10000000000.B }
|
||||
withLabel: mem20gb { memory = 20000000000.B }
|
||||
withLabel: mem50gb { memory = 50000000000.B }
|
||||
withLabel: mem100gb { memory = 100000000000.B }
|
||||
withLabel: mem200gb { memory = 200000000000.B }
|
||||
withLabel: mem500gb { memory = 500000000000.B }
|
||||
withLabel: mem1tb { memory = 1000000000000.B }
|
||||
withLabel: mem2tb { memory = 2000000000000.B }
|
||||
withLabel: mem5tb { memory = 5000000000000.B }
|
||||
withLabel: mem10tb { memory = 10000000000000.B }
|
||||
withLabel: mem20tb { memory = 20000000000000.B }
|
||||
withLabel: mem50tb { memory = 50000000000000.B }
|
||||
withLabel: mem100tb { memory = 100000000000000.B }
|
||||
withLabel: mem200tb { memory = 200000000000000.B }
|
||||
withLabel: mem500tb { memory = 500000000000000.B }
|
||||
withLabel: mem1gib { memory = 1073741824.B }
|
||||
withLabel: mem2gib { memory = 2147483648.B }
|
||||
withLabel: mem4gib { memory = 4294967296.B }
|
||||
withLabel: mem8gib { memory = 8589934592.B }
|
||||
withLabel: mem16gib { memory = 17179869184.B }
|
||||
withLabel: mem32gib { memory = 34359738368.B }
|
||||
withLabel: mem64gib { memory = 68719476736.B }
|
||||
withLabel: mem128gib { memory = 137438953472.B }
|
||||
withLabel: mem256gib { memory = 274877906944.B }
|
||||
withLabel: mem512gib { memory = 549755813888.B }
|
||||
withLabel: mem1tib { memory = 1099511627776.B }
|
||||
withLabel: mem2tib { memory = 2199023255552.B }
|
||||
withLabel: mem4tib { memory = 4398046511104.B }
|
||||
withLabel: mem8tib { memory = 8796093022208.B }
|
||||
withLabel: mem16tib { memory = 17592186044416.B }
|
||||
withLabel: mem32tib { memory = 35184372088832.B }
|
||||
withLabel: mem64tib { memory = 70368744177664.B }
|
||||
withLabel: mem128tib { memory = 140737488355328.B }
|
||||
withLabel: mem256tib { memory = 281474976710656.B }
|
||||
withLabel: mem512tib { memory = 562949953421312.B }
|
||||
withLabel: cpu1 { cpus = 1 }
|
||||
withLabel: cpu2 { cpus = 2 }
|
||||
withLabel: cpu5 { cpus = 5 }
|
||||
withLabel: cpu10 { cpus = 10 }
|
||||
withLabel: cpu20 { cpus = 20 }
|
||||
withLabel: cpu50 { cpus = 50 }
|
||||
withLabel: cpu100 { cpus = 100 }
|
||||
withLabel: cpu200 { cpus = 200 }
|
||||
withLabel: cpu500 { cpus = 500 }
|
||||
withLabel: cpu1000 { cpus = 1000 }
|
||||
}
|
||||
|
||||
|
||||
194
target/nextflow/csv2fasta/nextflow_schema.json
Normal file
194
target/nextflow/csv2fasta/nextflow_schema.json
Normal file
@@ -0,0 +1,194 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "csv2fasta",
|
||||
"description": "Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"inputs" : {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, example: `barcodes.csv`. CSV file to be processed",
|
||||
"help_text": "Type: `file`, required, example: `barcodes.csv`. CSV file to be processed."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"header": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Parse the first line of the CSV file as a header",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Parse the first line of the CSV file as a header.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"outputs" : {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output.fasta`, example: `barcodes.fasta`. Output fasta file",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output.fasta`, example: `barcodes.fasta`. Output fasta file."
|
||||
,
|
||||
"default": "$id.$key.output.fasta"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"csv dialect options" : {
|
||||
"title": "CSV dialect options",
|
||||
"type": "object",
|
||||
"description": "Options that can be used to override the automatically detected\ndialect of the CSV file.\n",
|
||||
"properties": {
|
||||
|
||||
|
||||
"delimiter": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. Overwrite the column delimiter character",
|
||||
"help_text": "Type: `string`. Overwrite the column delimiter character.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"quote_character": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. Overwrite the character used to denote the start and end of a quoted item",
|
||||
"help_text": "Type: `string`. Overwrite the character used to denote the start and end of a quoted item.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"csv column arguments" : {
|
||||
"title": "CSV column arguments",
|
||||
"type": "object",
|
||||
"description": "Parameters for the selection of columns from the CSV file.\nOnly required when your CSV file contains more than 2 columns,\notherwise the first column will be used for the FASTA header\nand the second for the FASTA nucleotide sequences. This default\ncan still be overwritten by using the options below.\n",
|
||||
"properties": {
|
||||
|
||||
|
||||
"sequence_column": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. Name of the column containing the sequences",
|
||||
"help_text": "Type: `string`. Name of the column containing the sequences. Implies \u0027header\u0027.\nCannot be used together with \u0027sequence_column_index\u0027.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"name_column": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. Name of the column describing the FASTA headers",
|
||||
"help_text": "Type: `string`. Name of the column describing the FASTA headers. Implies \u0027header\u0027.\nCannot be used together with \u0027name_column_index\u0027.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"sequence_column_index": {
|
||||
"type":
|
||||
"integer",
|
||||
"description": "Type: `integer`. Index of the column to use as the FASTA sequences, counter from the left and\nstarting from 0",
|
||||
"help_text": "Type: `integer`. Index of the column to use as the FASTA sequences, counter from the left and\nstarting from 0. Cannot be used in combination with the \u0027sequence_column\u0027 argument.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"name_column_index": {
|
||||
"type":
|
||||
"integer",
|
||||
"description": "Type: `integer`. Index of the column to use as the FASTA headers, counter from the left and\nstarting from 0",
|
||||
"help_text": "Type: `integer`. Index of the column to use as the FASTA headers, counter from the left and\nstarting from 0. Cannot be used in combination with \u0027name_column\u0027.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"param_list": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
||||
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
||||
"hidden": true
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/inputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/outputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/csv dialect options"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/csv column arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
173
target/nextflow/untar/.config.vsh.yaml
Normal file
173
target/nextflow/untar/.config.vsh.yaml
Normal file
@@ -0,0 +1,173 @@
|
||||
name: "untar"
|
||||
version: "v0.1"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Tarball file to be unpacked."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Directory to write the contents of the .tar file to."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Other arguments"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--exclude"
|
||||
alternatives:
|
||||
- "-e"
|
||||
description: "Prevents any file or member whose name matches the shell wildcard\
|
||||
\ (pattern) from being extracted."
|
||||
info: null
|
||||
example:
|
||||
- "docs/figures"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Unpack a .tar file. When the contents of the .tar file is just a single\
|
||||
\ directory,\nput the contents of the directory into the output folder instead of\
|
||||
\ that directory.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
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: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.1"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/untar/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/untar"
|
||||
executable: "target/nextflow/untar/main.nf"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "v0.1"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
|
||||
keywords:
|
||||
- "scripts"
|
||||
- "custom"
|
||||
- "implementations"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
issue_tracker: "https://github.com/viash-hub/craftbox/issues"
|
||||
3565
target/nextflow/untar/main.nf
Normal file
3565
target/nextflow/untar/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
125
target/nextflow/untar/nextflow.config
Normal file
125
target/nextflow/untar/nextflow.config
Normal file
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'untar'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.1'
|
||||
description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
// detect tempdir
|
||||
tempDir = java.nio.file.Paths.get(
|
||||
System.getenv('NXF_TEMP') ?:
|
||||
System.getenv('VIASH_TEMP') ?:
|
||||
System.getenv('TEMPDIR') ?:
|
||||
System.getenv('TMPDIR') ?:
|
||||
'/tmp'
|
||||
).toAbsolutePath()
|
||||
|
||||
profiles {
|
||||
no_publish {
|
||||
process {
|
||||
withName: '.*' {
|
||||
publishDir = [
|
||||
enabled: false
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
mount_temp {
|
||||
docker.temp = tempDir
|
||||
podman.temp = tempDir
|
||||
charliecloud.temp = tempDir
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
// docker.userEmulation = true
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
docker.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
podman {
|
||||
podman.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
shifter {
|
||||
shifter.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
charliecloud {
|
||||
charliecloud.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
}
|
||||
}
|
||||
|
||||
process{
|
||||
withLabel: mem1gb { memory = 1000000000.B }
|
||||
withLabel: mem2gb { memory = 2000000000.B }
|
||||
withLabel: mem5gb { memory = 5000000000.B }
|
||||
withLabel: mem10gb { memory = 10000000000.B }
|
||||
withLabel: mem20gb { memory = 20000000000.B }
|
||||
withLabel: mem50gb { memory = 50000000000.B }
|
||||
withLabel: mem100gb { memory = 100000000000.B }
|
||||
withLabel: mem200gb { memory = 200000000000.B }
|
||||
withLabel: mem500gb { memory = 500000000000.B }
|
||||
withLabel: mem1tb { memory = 1000000000000.B }
|
||||
withLabel: mem2tb { memory = 2000000000000.B }
|
||||
withLabel: mem5tb { memory = 5000000000000.B }
|
||||
withLabel: mem10tb { memory = 10000000000000.B }
|
||||
withLabel: mem20tb { memory = 20000000000000.B }
|
||||
withLabel: mem50tb { memory = 50000000000000.B }
|
||||
withLabel: mem100tb { memory = 100000000000000.B }
|
||||
withLabel: mem200tb { memory = 200000000000000.B }
|
||||
withLabel: mem500tb { memory = 500000000000000.B }
|
||||
withLabel: mem1gib { memory = 1073741824.B }
|
||||
withLabel: mem2gib { memory = 2147483648.B }
|
||||
withLabel: mem4gib { memory = 4294967296.B }
|
||||
withLabel: mem8gib { memory = 8589934592.B }
|
||||
withLabel: mem16gib { memory = 17179869184.B }
|
||||
withLabel: mem32gib { memory = 34359738368.B }
|
||||
withLabel: mem64gib { memory = 68719476736.B }
|
||||
withLabel: mem128gib { memory = 137438953472.B }
|
||||
withLabel: mem256gib { memory = 274877906944.B }
|
||||
withLabel: mem512gib { memory = 549755813888.B }
|
||||
withLabel: mem1tib { memory = 1099511627776.B }
|
||||
withLabel: mem2tib { memory = 2199023255552.B }
|
||||
withLabel: mem4tib { memory = 4398046511104.B }
|
||||
withLabel: mem8tib { memory = 8796093022208.B }
|
||||
withLabel: mem16tib { memory = 17592186044416.B }
|
||||
withLabel: mem32tib { memory = 35184372088832.B }
|
||||
withLabel: mem64tib { memory = 70368744177664.B }
|
||||
withLabel: mem128tib { memory = 140737488355328.B }
|
||||
withLabel: mem256tib { memory = 281474976710656.B }
|
||||
withLabel: mem512tib { memory = 562949953421312.B }
|
||||
withLabel: cpu1 { cpus = 1 }
|
||||
withLabel: cpu2 { cpus = 2 }
|
||||
withLabel: cpu5 { cpus = 5 }
|
||||
withLabel: cpu10 { cpus = 10 }
|
||||
withLabel: cpu20 { cpus = 20 }
|
||||
withLabel: cpu50 { cpus = 50 }
|
||||
withLabel: cpu100 { cpus = 100 }
|
||||
withLabel: cpu200 { cpus = 200 }
|
||||
withLabel: cpu500 { cpus = 500 }
|
||||
withLabel: cpu1000 { cpus = 1000 }
|
||||
}
|
||||
|
||||
|
||||
119
target/nextflow/untar/nextflow_schema.json
Normal file
119
target/nextflow/untar/nextflow_schema.json
Normal file
@@ -0,0 +1,119 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "untar",
|
||||
"description": "Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. Tarball file to be unpacked",
|
||||
"help_text": "Type: `file`, required. Tarball file to be unpacked."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"output arguments" : {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the .tar file to."
|
||||
,
|
||||
"default": "$id.$key.output.output"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"other arguments" : {
|
||||
"title": "Other arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"exclude": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `docs/figures`. Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted",
|
||||
"help_text": "Type: `string`, example: `docs/figures`. Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"param_list": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
||||
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
||||
"hidden": true
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/input arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/output arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/other arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
Reference in New Issue
Block a user