Build branch main with version main (ed860be)
Build pipeline: vsh-ci-template-hp9jh
Source commit: ed860bed30
Source message: BUG: Wrong pointer to biobox dependency (#15)
* Fix pointer to biobox
* Add PR number
This commit is contained in:
169
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
Normal file
169
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
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@@ -0,0 +1,169 @@
|
||||
name: "combine_samples"
|
||||
namespace: "dataflow"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--id"
|
||||
description: "ID of the new event"
|
||||
info: null
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--forward_input"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--reverse_input"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_forward"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_reverse"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "nextflow_script"
|
||||
path: "main.nf"
|
||||
is_executable: true
|
||||
entrypoint: "run_wf"
|
||||
description: "Combine fastq files from across samples into one event with a list of\
|
||||
\ fastq files per orientation."
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
runners:
|
||||
- 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: "native"
|
||||
id: "native"
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/combine_samples/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "native|native"
|
||||
output: "target/nextflow/dataflow/combine_samples"
|
||||
executable: "target/nextflow/dataflow/combine_samples/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
|
||||
dest: "test_resources"
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "demultiplexing"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
|
||||
3155
target/nextflow/dataflow/combine_samples/main.nf
Normal file
3155
target/nextflow/dataflow/combine_samples/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
125
target/nextflow/dataflow/combine_samples/nextflow.config
Normal file
125
target/nextflow/dataflow/combine_samples/nextflow.config
Normal file
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'dataflow/combine_samples'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
|
||||
}
|
||||
|
||||
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 }
|
||||
}
|
||||
|
||||
|
||||
126
target/nextflow/dataflow/combine_samples/nextflow_schema.json
Normal file
126
target/nextflow/dataflow/combine_samples/nextflow_schema.json
Normal file
@@ -0,0 +1,126 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "combine_samples",
|
||||
"description": "Combine fastq files from across samples into one event with a list of fastq files per orientation.",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"id": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required. ID of the new event",
|
||||
"help_text": "Type: `string`, required. ID of the new event"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"forward_input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. ",
|
||||
"help_text": "Type: `file`, required. "
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"reverse_input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`. ",
|
||||
"help_text": "Type: `file`. "
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"output arguments" : {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output_forward": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. ",
|
||||
"help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. "
|
||||
,
|
||||
"default": "$id.$key.output_forward_*.output_forward_*"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_reverse": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. ",
|
||||
"help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. "
|
||||
,
|
||||
"default": "$id.$key.output_reverse_*.output_reverse_*"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"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"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -0,0 +1,163 @@
|
||||
name: "gather_fastqs_and_validate"
|
||||
namespace: "dataflow"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Directory containing .fastq files"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_sheet"
|
||||
description: "Sample sheet"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--fastq_forward"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastq_reverse"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "nextflow_script"
|
||||
path: "main.nf"
|
||||
is_executable: true
|
||||
entrypoint: "run_wf"
|
||||
description: "From a directory containing fastq files, gather the files per sample\
|
||||
\ \nand validate according to the contents of the sample sheet.\n"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
runners:
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "native"
|
||||
id: "native"
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/gather_fastqs_and_validate/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "native|native"
|
||||
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
|
||||
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
|
||||
dest: "test_resources"
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "demultiplexing"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
|
||||
3193
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
Normal file
3193
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'dataflow/gather_fastqs_and_validate'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\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 }
|
||||
}
|
||||
|
||||
|
||||
@@ -0,0 +1,116 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "gather_fastqs_and_validate",
|
||||
"description": "From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. Directory containing ",
|
||||
"help_text": "Type: `file`, required. Directory containing .fastq files"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"sample_sheet": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. Sample sheet",
|
||||
"help_text": "Type: `file`, required. Sample sheet"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"output arguments" : {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"fastq_forward": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.fastq_forward.fastq_forward`. ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.fastq_forward.fastq_forward`. "
|
||||
,
|
||||
"default": "$id.$key.fastq_forward.fastq_forward"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"fastq_reverse": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.fastq_reverse.fastq_reverse`. ",
|
||||
"help_text": "Type: `file`, default: `$id.$key.fastq_reverse.fastq_reverse`. "
|
||||
,
|
||||
"default": "$id.$key.fastq_reverse.fastq_reverse"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"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"
|
||||
}
|
||||
]
|
||||
}
|
||||
224
target/nextflow/demultiplex/.config.vsh.yaml
Normal file
224
target/nextflow/demultiplex/.config.vsh.yaml
Normal file
@@ -0,0 +1,224 @@
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Directory containing raw sequencing data"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_sheet"
|
||||
description: "Sample sheet as input for BCL Convert. If not specified,\nwill try\
|
||||
\ to autodetect the sample sheet in the input directory\n"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Directory to write fastq data to"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_falco"
|
||||
description: "Directory to write falco output to"
|
||||
info: null
|
||||
default:
|
||||
- "$id/falco"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_multiqc"
|
||||
description: "Directory to write falco output to"
|
||||
info: null
|
||||
default:
|
||||
- "$id/multiqc_report.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "nextflow_script"
|
||||
path: "main.nf"
|
||||
is_executable: true
|
||||
entrypoint: "run_wf"
|
||||
description: "Demultiplexing of raw sequencing data"
|
||||
test_resources:
|
||||
- type: "nextflow_script"
|
||||
path: "test.nf"
|
||||
is_executable: true
|
||||
entrypoint: "test_wf"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
dependencies:
|
||||
- name: "io/untar"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "dataflow/gather_fastqs_and_validate"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "io/interop_summary_to_csv"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "dataflow/combine_samples"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "bcl_convert"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "v0.1.0"
|
||||
- name: "falco"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "v0.1.0"
|
||||
- name: "multiqc"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "v0.1.0"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "bb"
|
||||
repo: "biobox"
|
||||
tag: "v0.1.0"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
runners:
|
||||
- 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: "native"
|
||||
id: "native"
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/demultiplex/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "native|native"
|
||||
output: "target/nextflow/demultiplex"
|
||||
executable: "target/nextflow/demultiplex/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
dependencies:
|
||||
- "target/nextflow/io/untar"
|
||||
- "target/nextflow/dataflow/gather_fastqs_and_validate"
|
||||
- "target/nextflow/io/interop_summary_to_csv"
|
||||
- "target/nextflow/dataflow/combine_samples"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
|
||||
dest: "test_resources"
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "demultiplexing"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
|
||||
3343
target/nextflow/demultiplex/main.nf
Normal file
3343
target/nextflow/demultiplex/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
125
target/nextflow/demultiplex/nextflow.config
Normal file
125
target/nextflow/demultiplex/nextflow.config
Normal file
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'demultiplex'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
description = 'Demultiplexing of raw sequencing data'
|
||||
}
|
||||
|
||||
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 }
|
||||
}
|
||||
|
||||
|
||||
127
target/nextflow/demultiplex/nextflow_schema.json
Normal file
127
target/nextflow/demultiplex/nextflow_schema.json
Normal file
@@ -0,0 +1,127 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "demultiplex",
|
||||
"description": "Demultiplexing of raw sequencing data",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. Directory containing raw sequencing data",
|
||||
"help_text": "Type: `file`, required. Directory containing raw sequencing data"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"sample_sheet": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`. Sample sheet as input for BCL Convert",
|
||||
"help_text": "Type: `file`. Sample sheet as input for BCL Convert. If not specified,\nwill try to autodetect the sample sheet in the input directory\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"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 fastq data to",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write fastq data to"
|
||||
,
|
||||
"default": "$id.$key.output.output"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_falco": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output_falco.output_falco`. Directory to write falco output to",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output_falco.output_falco`. Directory to write falco output to"
|
||||
,
|
||||
"default": "$id.$key.output_falco.output_falco"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_multiqc": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to"
|
||||
,
|
||||
"default": "$id.$key.output_multiqc.html"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"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"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
171
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
Normal file
171
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
Normal file
@@ -0,0 +1,171 @@
|
||||
name: "interop_summary_to_csv"
|
||||
namespace: "io"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Sequencing run folder (*not* InterOp folder)."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_run_summary"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_index_summary"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$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: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
- "wget"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "wget https://github.com/Illumina/interop/releases/download/v1.3.1/interop-1.3.1-Linux-GNU.tar.gz\
|
||||
\ -O /tmp/interop.tar.gz && \\\ntar -C /tmp/ --no-same-owner --no-same-permissions\
|
||||
\ -xvf /tmp/interop.tar.gz && \\\nmv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary\
|
||||
\ /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/io/interop_summary_to_csv/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/io/interop_summary_to_csv"
|
||||
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
|
||||
dest: "test_resources"
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "demultiplexing"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
|
||||
3513
target/nextflow/io/interop_summary_to_csv/main.nf
Normal file
3513
target/nextflow/io/interop_summary_to_csv/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
124
target/nextflow/io/interop_summary_to_csv/nextflow.config
Normal file
124
target/nextflow/io/interop_summary_to_csv/nextflow.config
Normal file
@@ -0,0 +1,124 @@
|
||||
manifest {
|
||||
name = 'io/interop_summary_to_csv'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
}
|
||||
|
||||
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/io/interop_summary_to_csv/nextflow_schema.json
Normal file
106
target/nextflow/io/interop_summary_to_csv/nextflow_schema.json
Normal file
@@ -0,0 +1,106 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "interop_summary_to_csv",
|
||||
"description": "No description",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"input arguments" : {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required. Sequencing run folder (*not* InterOp folder)",
|
||||
"help_text": "Type: `file`, required. Sequencing run folder (*not* InterOp folder)."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"output arguments" : {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output_run_summary": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. "
|
||||
,
|
||||
"default": "$id.$key.output_run_summary.output_run_summary"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_index_summary": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. "
|
||||
,
|
||||
"default": "$id.$key.output_index_summary.output_index_summary"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"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"
|
||||
}
|
||||
]
|
||||
}
|
||||
178
target/nextflow/io/untar/.config.vsh.yaml
Normal file
178
target/nextflow/io/untar/.config.vsh.yaml
Normal file
@@ -0,0 +1,178 @@
|
||||
name: "untar"
|
||||
namespace: "io"
|
||||
version: "main"
|
||||
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/demultiplex"
|
||||
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: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/io/untar/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/io/untar"
|
||||
executable: "target/nextflow/io/untar/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "main"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
|
||||
dest: "test_resources"
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "demultiplexing"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/demultiplex"
|
||||
issue_tracker: "https://github.com/viash-hub/demultiplex/issues"
|
||||
3555
target/nextflow/io/untar/main.nf
Normal file
3555
target/nextflow/io/untar/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
125
target/nextflow/io/untar/nextflow.config
Normal file
125
target/nextflow/io/untar/nextflow.config
Normal file
@@ -0,0 +1,125 @@
|
||||
manifest {
|
||||
name = 'io/untar'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
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/io/untar/nextflow_schema.json
Normal file
119
target/nextflow/io/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