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Build branch main with version main (399e469)

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Build pipeline: viash-hub.demultiplex.main-f55jt

Source commit: 399e46901d

Source message: Add test_resources to .gitignore
This commit is contained in:
CI
2024-09-13 09:46:12 +00:00
parent 6c37efac8f
commit ebd9b69856
30 changed files with 482 additions and 212 deletions
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3
.gitignore vendored
View File

@@ -1,7 +1,8 @@
target
testData
test_resources
# Nextflow related files
.nextflow
.nextflow.log*
work
work

18
CHANGELOG.md
View File

@@ -1,17 +1,13 @@
# 0.1.2
# Unreleased
## NEW FEATURES
## Minor updates
* Bump viash to 0.9.0 (PR #14).
* `demultiplex` workflow: use `v0.2.0` release instead of `main` branch for `biobox` dependencies (PR #11).
* Renamed `biobase` repository to `biobox` (PR #13 and PR #15).
* Bump viash to 0.9.0-RC6 (PR #14).
# v0.1.1
## NEW FEATURES
* `demultiplex` workflow: use `v0.1.0` release instead of `main` branch for `biobase` dependencies (PR #11).
# v0.1.0
Initial release
Initial release

2
src/demultiplex/config.vsh.yaml
View File

@@ -61,7 +61,7 @@ repositories:
- name: bb
type: vsh
repo: biobox
tag: v0.1.0
tag: v0.2.0
runners:
- type: nextflow

48
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml
View File

@@ -1,5 +1,30 @@
name: "bcl_convert"
version: "v0.1.0"
version: "0.2.0"
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: "Dorien Roosen"
roles:
- "author"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Input arguments"
arguments:
@@ -281,9 +306,16 @@ status: "enabled"
requirements:
commands:
- "ps"
license: "MIT"
keywords:
- "demultiplex"
- "fastq"
- "bcl"
- "illumina"
license: "Proprietary"
links:
repository: "https://github.com/viash-hub/biobox"
homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.html"
runners:
- type: "executable"
id: "executable"
@@ -354,7 +386,7 @@ engines:
id: "docker"
image: "debian:trixie-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "0.2.0"
namespace_separator: "/"
setup:
- type: "apt"
@@ -385,22 +417,22 @@ build_info:
engine: "docker|native"
output: "target/nextflow/bcl_convert"
executable: "target/nextflow/bcl_convert/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
viash_version: "0.9.0"
git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "v0.1.0"
version: "0.2.0"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := '0.2.0'"
keywords:
- "bioinformatics"
- "modules"

149
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf
View File

@@ -1,13 +1,17 @@
// bcl_convert v0.1.0
// bcl_convert 0.2.0
//
// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
// Data Intuitive.
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
// Intuitive.
//
// The component may contain files which fall under a different license. The
// authors of this component should specify the license in the header of such
// files, or include a separate license file detailing the licenses of all included
// files.
//
// Component authors:
// * Toni Verbeiren (author, maintainer)
// * Dorien Roosen (author)
////////////////////////////
// VDSL3 helper functions //
@@ -760,8 +764,11 @@ def runEach(Map args) {
def fromState_ = args.fromState
def toState_ = args.toState
def filter_ = args.filter
def runIf_ = args.runIf
def id_ = args.id
assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
workflow runEachWf {
take: input_ch
main:
@@ -783,7 +790,20 @@ def runEach(Map args) {
[new_id] + tup.drop(1)
}
: filter_ch
def data_ch = id_ch | map{tup ->
def chPassthrough = null
def chRun = null
if (runIf_) {
def idRunIfBranch = id_ch.branch{ tup ->
run: runIf_(tup[0], tup[1], comp_)
passthrough: true
}
chPassthrough = idRunIfBranch.passthrough
chRun = idRunIfBranch.run
} else {
chRun = id_ch
chPassthrough = Channel.empty()
}
def data_ch = chRun | map{tup ->
def new_data = tup[1]
if (fromState_ instanceof Map) {
new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +841,11 @@ def runEach(Map args) {
[tup[0], new_state] + tup.drop(3)
}
: out_ch
def return_ch = post_ch
| concat(chPassthrough)
post_ch
return_ch
}
// mix all results
@@ -1598,8 +1621,8 @@ def findStates(Map params, Map config) {
// construct renameMap
if (args.rename_keys) {
def renameMap = args.rename_keys.collectEntries{renameString ->
def split = renameString.split(";")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
def split = renameString.split(":")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
split
}
@@ -1709,7 +1732,9 @@ def publishStates(Map args) {
def yamlFilename = yamlTemplate_
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
// TODO: do the pathnames in state_ match up with the outputFilenames_?
@@ -1780,7 +1805,9 @@ def publishStatesByConfig(Map args) {
def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
def yamlFilename = yamlTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
// the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1849,9 @@ def publishStatesByConfig(Map args) {
// instantiate the template
def filename = filenameTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
if (par.multiple) {
// if the parameter is multiple: true, the filename
// should contain a wildcard '*' that is replaced with
@@ -2626,30 +2655,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
tuple
}
def chModifiedFiltered = workflowArgs.filter ?
chModified | filter{workflowArgs.filter(it)} :
chModified
def chRun = null
def chPassthrough = null
if (workflowArgs.runIf) {
def runIfBranch = chModifiedFiltered.branch{ tup ->
def runIfBranch = chModified.branch{ tup ->
run: workflowArgs.runIf(tup[0], tup[1])
passthrough: true
}
chRun = runIfBranch.run
chPassthrough = runIfBranch.passthrough
} else {
chRun = chModifiedFiltered
chRun = chModified
chPassthrough = Channel.empty()
}
def chRunFiltered = workflowArgs.filter ?
chRun | filter{workflowArgs.filter(it)} :
chRun
def chArgs = workflowArgs.fromState ?
chRun | map{
chRunFiltered | map{
def new_data = workflowArgs.fromState(it.take(2))
[it[0], new_data]
} :
chRun | map {tup -> tup.take(2)}
chRunFiltered | map {tup -> tup.take(2)}
// fill in defaults
def chArgsWithDefaults = chArgs
@@ -2720,7 +2750,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
// | view{"chInitialOutput: ${it.take(3)}"}
// join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
// input tuple format: [join_id, id, output, prev_state, ...]
// output tuple format: [join_id, id, new_state, ...]
| map{ tup ->
@@ -2779,7 +2809,49 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "bcl_convert",
"version" : "v0.1.0",
"version" : "0.2.0",
"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" : "Dorien Roosen",
"roles" : [
"author"
],
"info" : {
"links" : {
"email" : "dorien@data-intuitive.com",
"github" : "dorien-er",
"linkedin" : "dorien-roosen"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Scientist"
}
]
}
}
],
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3125,9 +3197,17 @@ meta = [
"ps"
]
},
"license" : "MIT",
"keywords" : [
"demultiplex",
"fastq",
"bcl",
"illumina"
],
"license" : "Proprietary",
"links" : {
"repository" : "https://github.com/viash-hub/biobox"
"repository" : "https://github.com/viash-hub/biobox",
"homepage" : "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html",
"documentation" : "https://support.illumina.com/downloads/bcl-convert-user-guide.html"
},
"runners" : [
{
@@ -3209,7 +3289,7 @@ meta = [
"id" : "docker",
"image" : "debian:trixie-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "0.2.0",
"namespace_separator" : "/",
"setup" : [
{
@@ -3248,22 +3328,22 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/bcl_convert",
"viash_version" : "0.9.0-RC6",
"git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
"viash_version" : "0.9.0",
"git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.1.0",
"version" : "0.2.0",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.1.0'"
".engines[.type == 'docker'].target_tag := '0.2.0'"
],
"keywords" : [
"bioinformatics",
@@ -3454,7 +3534,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
val = val.join(par.multiple_sep)
}
if (par.direction == "output" && par.type == "file") {
val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
val = val
.replaceAll('\\$id', id)
.replaceAll('\\$\\{id\\}', id)
.replaceAll('\\$key', key)
.replaceAll('\\$\\{key\\}', key)
}
[parName, val]
}
@@ -3585,7 +3669,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def createParentStr = meta.config.allArguments
.findAll { it.type == "file" && it.direction == "output" && it.create_parent }
.collect { par ->
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
}
.join("\n")
@@ -3593,8 +3678,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def inputFileExports = meta.config.allArguments
.findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
.collect { par ->
def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
}
// NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3631,6 +3716,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def procStr =
"""nextflow.enable.dsl=2
|
|def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
|process $procKey {$drctvStrs
|input:
| tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3642,10 +3728,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
|$stub
|\"\"\"
|script:$assertStr
|def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
|def parInject = args
| .findAll{key, value -> value != null}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
| .join("\\n")
|\"\"\"
|# meta exports
@@ -3730,7 +3815,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/bcl_convert",
"tag" : "v0.1.0"
"tag" : "0.2.0"
},
"tag" : "$id"
}'''),

3
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow.config → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config
View File

@@ -2,8 +2,9 @@ manifest {
name = 'bcl_convert'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = '0.2.0'
description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n'
author = 'Toni Verbeiren, Dorien Roosen'
}
process.container = 'nextflow/bash:latest'

0
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow_schema.json
View File

27
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml
View File

@@ -1,5 +1,18 @@
name: "falco"
version: "v0.1.0"
version: "0.2.0"
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"
argument_groups:
- name: "Input arguments"
arguments:
@@ -274,7 +287,7 @@ engines:
id: "docker"
image: "debian:trixie-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "0.2.0"
namespace_separator: "/"
setup:
- type: "apt"
@@ -303,22 +316,22 @@ build_info:
engine: "docker|native"
output: "target/nextflow/falco"
executable: "target/nextflow/falco/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
viash_version: "0.9.0"
git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "v0.1.0"
version: "0.2.0"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := '0.2.0'"
keywords:
- "bioinformatics"
- "modules"

116
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf
View File

@@ -1,13 +1,16 @@
// falco v0.1.0
// falco 0.2.0
//
// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
// Data Intuitive.
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
// Intuitive.
//
// The component may contain files which fall under a different license. The
// authors of this component should specify the license in the header of such
// files, or include a separate license file detailing the licenses of all included
// files.
//
// Component authors:
// * Toni Verbeiren (author, maintainer)
////////////////////////////
// VDSL3 helper functions //
@@ -760,8 +763,11 @@ def runEach(Map args) {
def fromState_ = args.fromState
def toState_ = args.toState
def filter_ = args.filter
def runIf_ = args.runIf
def id_ = args.id
assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
workflow runEachWf {
take: input_ch
main:
@@ -783,7 +789,20 @@ def runEach(Map args) {
[new_id] + tup.drop(1)
}
: filter_ch
def data_ch = id_ch | map{tup ->
def chPassthrough = null
def chRun = null
if (runIf_) {
def idRunIfBranch = id_ch.branch{ tup ->
run: runIf_(tup[0], tup[1], comp_)
passthrough: true
}
chPassthrough = idRunIfBranch.passthrough
chRun = idRunIfBranch.run
} else {
chRun = id_ch
chPassthrough = Channel.empty()
}
def data_ch = chRun | map{tup ->
def new_data = tup[1]
if (fromState_ instanceof Map) {
new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +840,11 @@ def runEach(Map args) {
[tup[0], new_state] + tup.drop(3)
}
: out_ch
def return_ch = post_ch
| concat(chPassthrough)
post_ch
return_ch
}
// mix all results
@@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) {
// construct renameMap
if (args.rename_keys) {
def renameMap = args.rename_keys.collectEntries{renameString ->
def split = renameString.split(";")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
def split = renameString.split(":")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
split
}
@@ -1709,7 +1731,9 @@ def publishStates(Map args) {
def yamlFilename = yamlTemplate_
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
// TODO: do the pathnames in state_ match up with the outputFilenames_?
@@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) {
def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
def yamlFilename = yamlTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
// the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) {
// instantiate the template
def filename = filenameTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
if (par.multiple) {
// if the parameter is multiple: true, the filename
// should contain a wildcard '*' that is replaced with
@@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
tuple
}
def chModifiedFiltered = workflowArgs.filter ?
chModified | filter{workflowArgs.filter(it)} :
chModified
def chRun = null
def chPassthrough = null
if (workflowArgs.runIf) {
def runIfBranch = chModifiedFiltered.branch{ tup ->
def runIfBranch = chModified.branch{ tup ->
run: workflowArgs.runIf(tup[0], tup[1])
passthrough: true
}
chRun = runIfBranch.run
chPassthrough = runIfBranch.passthrough
} else {
chRun = chModifiedFiltered
chRun = chModified
chPassthrough = Channel.empty()
}
def chRunFiltered = workflowArgs.filter ?
chRun | filter{workflowArgs.filter(it)} :
chRun
def chArgs = workflowArgs.fromState ?
chRun | map{
chRunFiltered | map{
def new_data = workflowArgs.fromState(it.take(2))
[it[0], new_data]
} :
chRun | map {tup -> tup.take(2)}
chRunFiltered | map {tup -> tup.take(2)}
// fill in defaults
def chArgsWithDefaults = chArgs
@@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
// | view{"chInitialOutput: ${it.take(3)}"}
// join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
// input tuple format: [join_id, id, output, prev_state, ...]
// output tuple format: [join_id, id, new_state, ...]
| map{ tup ->
@@ -2779,7 +2808,29 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "falco",
"version" : "v0.1.0",
"version" : "0.2.0",
"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"
}
]
}
}
],
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3080,7 +3131,7 @@ meta = [
"id" : "docker",
"image" : "debian:trixie-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "0.2.0",
"namespace_separator" : "/",
"setup" : [
{
@@ -3118,22 +3169,22 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/falco",
"viash_version" : "0.9.0-RC6",
"git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
"viash_version" : "0.9.0",
"git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.1.0",
"version" : "0.2.0",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.1.0'"
".engines[.type == 'docker'].target_tag := '0.2.0'"
],
"keywords" : [
"bioinformatics",
@@ -3298,7 +3349,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
val = val.join(par.multiple_sep)
}
if (par.direction == "output" && par.type == "file") {
val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
val = val
.replaceAll('\\$id', id)
.replaceAll('\\$\\{id\\}', id)
.replaceAll('\\$key', key)
.replaceAll('\\$\\{key\\}', key)
}
[parName, val]
}
@@ -3429,7 +3484,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def createParentStr = meta.config.allArguments
.findAll { it.type == "file" && it.direction == "output" && it.create_parent }
.collect { par ->
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
}
.join("\n")
@@ -3437,8 +3493,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def inputFileExports = meta.config.allArguments
.findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
.collect { par ->
def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
}
// NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3475,6 +3531,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def procStr =
"""nextflow.enable.dsl=2
|
|def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
|process $procKey {$drctvStrs
|input:
| tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3486,10 +3543,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
|$stub
|\"\"\"
|script:$assertStr
|def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
|def parInject = args
| .findAll{key, value -> value != null}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
| .join("\\n")
|\"\"\"
|# meta exports
@@ -3574,7 +3630,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/falco",
"tag" : "v0.1.0"
"tag" : "0.2.0"
},
"tag" : "$id"
}'''),

3
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow.config → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config
View File

@@ -2,8 +2,9 @@ manifest {
name = 'falco'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = '0.2.0'
description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data'
author = 'Toni Verbeiren'
}
process.container = 'nextflow/bash:latest'

4
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json
View File

@@ -17,8 +17,8 @@
"input": {
"type":
"string",
"description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files",
"help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files"
"description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files",
"help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files"
}

48
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml
View File

@@ -1,5 +1,19 @@
name: "multiqc"
version: "v0.1.0"
version: "0.2.0"
authors:
- name: "Dorien Roosen"
roles:
- "author"
- "maintainer"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Input"
arguments:
@@ -63,39 +77,43 @@ argument_groups:
description: "Use only these module"
info: null
example:
- "fastqc,cutadapt"
- "fastqc"
- "cutadapt"
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "string"
name: "--exclude_modules"
description: "Do not use only these modules"
info: null
example:
- "fastqc,cutadapt"
- "fastqc"
- "cutadapt"
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "string"
name: "--ignore_analysis"
info: null
example:
- "run_one/*,run_two/*"
- "run_one/*"
- "run_two/*"
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "string"
name: "--ignore_samples"
info: null
example:
- "sample_1*,sample_3*"
- "sample_1*"
- "sample_3*"
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "boolean_true"
name: "--ignore_symlinks"
description: "Ignore symlinked directories and files"
@@ -415,7 +433,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "0.2.0"
namespace_separator: "/"
setup:
- type: "docker"
@@ -437,22 +455,22 @@ build_info:
engine: "docker|native"
output: "target/nextflow/multiqc"
executable: "target/nextflow/multiqc/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
viash_version: "0.9.0"
git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "v0.1.0"
version: "0.2.0"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := '0.2.0'"
keywords:
- "bioinformatics"
- "modules"

189
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf
View File

@@ -1,13 +1,16 @@
// multiqc v0.1.0
// multiqc 0.2.0
//
// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
// Data Intuitive.
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
// Intuitive.
//
// The component may contain files which fall under a different license. The
// authors of this component should specify the license in the header of such
// files, or include a separate license file detailing the licenses of all included
// files.
//
// Component authors:
// * Dorien Roosen (author, maintainer)
////////////////////////////
// VDSL3 helper functions //
@@ -760,8 +763,11 @@ def runEach(Map args) {
def fromState_ = args.fromState
def toState_ = args.toState
def filter_ = args.filter
def runIf_ = args.runIf
def id_ = args.id
assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
workflow runEachWf {
take: input_ch
main:
@@ -783,7 +789,20 @@ def runEach(Map args) {
[new_id] + tup.drop(1)
}
: filter_ch
def data_ch = id_ch | map{tup ->
def chPassthrough = null
def chRun = null
if (runIf_) {
def idRunIfBranch = id_ch.branch{ tup ->
run: runIf_(tup[0], tup[1], comp_)
passthrough: true
}
chPassthrough = idRunIfBranch.passthrough
chRun = idRunIfBranch.run
} else {
chRun = id_ch
chPassthrough = Channel.empty()
}
def data_ch = chRun | map{tup ->
def new_data = tup[1]
if (fromState_ instanceof Map) {
new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +840,11 @@ def runEach(Map args) {
[tup[0], new_state] + tup.drop(3)
}
: out_ch
def return_ch = post_ch
| concat(chPassthrough)
post_ch
return_ch
}
// mix all results
@@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) {
// construct renameMap
if (args.rename_keys) {
def renameMap = args.rename_keys.collectEntries{renameString ->
def split = renameString.split(";")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
def split = renameString.split(":")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
split
}
@@ -1709,7 +1731,9 @@ def publishStates(Map args) {
def yamlFilename = yamlTemplate_
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
// TODO: do the pathnames in state_ match up with the outputFilenames_?
@@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) {
def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
def yamlFilename = yamlTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
// the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) {
// instantiate the template
def filename = filenameTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
if (par.multiple) {
// if the parameter is multiple: true, the filename
// should contain a wildcard '*' that is replaced with
@@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
tuple
}
def chModifiedFiltered = workflowArgs.filter ?
chModified | filter{workflowArgs.filter(it)} :
chModified
def chRun = null
def chPassthrough = null
if (workflowArgs.runIf) {
def runIfBranch = chModifiedFiltered.branch{ tup ->
def runIfBranch = chModified.branch{ tup ->
run: workflowArgs.runIf(tup[0], tup[1])
passthrough: true
}
chRun = runIfBranch.run
chPassthrough = runIfBranch.passthrough
} else {
chRun = chModifiedFiltered
chRun = chModified
chPassthrough = Channel.empty()
}
def chRunFiltered = workflowArgs.filter ?
chRun | filter{workflowArgs.filter(it)} :
chRun
def chArgs = workflowArgs.fromState ?
chRun | map{
chRunFiltered | map{
def new_data = workflowArgs.fromState(it.take(2))
[it[0], new_data]
} :
chRun | map {tup -> tup.take(2)}
chRunFiltered | map {tup -> tup.take(2)}
// fill in defaults
def chArgsWithDefaults = chArgs
@@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
// | view{"chInitialOutput: ${it.take(3)}"}
// join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
// input tuple format: [join_id, id, output, prev_state, ...]
// output tuple format: [join_id, id, new_state, ...]
| map{ tup ->
@@ -2779,7 +2808,30 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "multiqc",
"version" : "v0.1.0",
"version" : "0.2.0",
"authors" : [
{
"name" : "Dorien Roosen",
"roles" : [
"author",
"maintainer"
],
"info" : {
"links" : {
"email" : "dorien@data-intuitive.com",
"github" : "dorien-er",
"linkedin" : "dorien-roosen"
},
"organizations" : [
{
"name" : "Data Intuitive",
"href" : "https://www.data-intuitive.com",
"role" : "Data Scientist"
}
]
}
}
],
"argument_groups" : [
{
"name" : "Input",
@@ -2855,46 +2907,50 @@ meta = [
"name" : "--include_modules",
"description" : "Use only these module",
"example" : [
"fastqc,cutadapt"
"fastqc",
"cutadapt"
],
"required" : false,
"direction" : "input",
"multiple" : true,
"multiple_sep" : ","
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--exclude_modules",
"description" : "Do not use only these modules",
"example" : [
"fastqc,cutadapt"
"fastqc",
"cutadapt"
],
"required" : false,
"direction" : "input",
"multiple" : true,
"multiple_sep" : ","
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--ignore_analysis",
"example" : [
"run_one/*,run_two/*"
"run_one/*",
"run_two/*"
],
"required" : false,
"direction" : "input",
"multiple" : true,
"multiple_sep" : ","
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--ignore_samples",
"example" : [
"sample_1*,sample_3*"
"sample_1*",
"sample_3*"
],
"required" : false,
"direction" : "input",
"multiple" : true,
"multiple_sep" : ","
"multiple_sep" : ";"
},
{
"type" : "boolean_true",
@@ -3279,7 +3335,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "0.2.0",
"namespace_separator" : "/",
"setup" : [
{
@@ -3309,22 +3365,22 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/multiqc",
"viash_version" : "0.9.0-RC6",
"git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
"viash_version" : "0.9.0",
"git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.1.0",
"version" : "0.2.0",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.1.0'"
".engines[.type == 'docker'].target_tag := '0.2.0'"
],
"keywords" : [
"bioinformatics",
@@ -3411,26 +3467,32 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
#!/bin/bash
# disable flags
[[ "\\$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks
[[ "\\$par_dirs" == "false" ]] && unset par_dirs
[[ "\\$par_full_names" == "false" ]] && unset par_full_names
[[ "\\$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
[[ "\\$par_profile_runtime" == "false" ]] && unset par_profile_runtime
[[ "\\$par_verbose" == "false" ]] && unset par_verbose
[[ "\\$par_quiet" == "false" ]] && unset par_quiet
[[ "\\$par_strict" == "false" ]] && unset par_strict
[[ "\\$par_development" == "false" ]] && unset par_development
[[ "\\$par_require_logs" == "false" ]] && unset par_require_logs
[[ "\\$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload
[[ "\\$par_no_ansi" == "false" ]] && unset par_no_ansi
[[ "\\$par_flat" == "false" ]] && unset par_flat
[[ "\\$par_interactive" == "false" ]] && unset par_interactive
[[ "\\$par_static_plot_export" == "false" ]] && unset par_static_plot_export
[[ "\\$par_data_dir" == "false" ]] && unset par_data_dir
[[ "\\$par_no_data_dir" == "false" ]] && unset par_no_data_dir
[[ "\\$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir
[[ "\\$par_pdf" == "false" ]] && unset par_pdf
unset_if_false=(
par_ignore_symlinks
par_dirs
par_full_names
par_fn_as_s_name
par_profile_runtime
par_verbose
par_quiet
par_strict
par_development
par_require_logs
par_no_megaqc_upload
par_no_ansi
par_flat
par_interactive
par_static_plot_export
par_data_dir
par_no_data_dir
par_zip_data_dir
par_pdf
)
for par in \\${unset_if_false[@]}; do
test_val="\\${!par}"
[[ "\\$test_val" == "false" ]] && unset \\$par
done
# handle inputs
out_dir=\\$(dirname "\\$par_output_report")
@@ -3448,7 +3510,7 @@ IFS=";" read -ra inputs <<< \\$par_input
if [[ -n "\\$par_include_modules" ]]; then
include_modules=""
IFS="," read -ra incl_modules <<< \\$par_include_modules
IFS=";" read -ra incl_modules <<< \\$par_include_modules
for i in "\\${incl_modules[@]}"; do
include_modules+="--include \\$i "
done
@@ -3457,7 +3519,7 @@ fi
if [[ -n "\\$par_exclude_modules" ]]; then
exclude_modules=""
IFS="," read -ra excl_modules <<< \\$par_exclude_modules
IFS=";" read -ra excl_modules <<< \\$par_exclude_modules
for i in "\\${excl_modules[@]}"; do
exclude_modules+="--exclude \\$i"
done
@@ -3466,7 +3528,7 @@ fi
if [[ -n "\\$par_ignore_analysis" ]]; then
ignore=""
IFS="," read -ra ignore_analysis <<< \\$par_ignore_analysis
IFS=";" read -ra ignore_analysis <<< \\$par_ignore_analysis
for i in "\\${ignore_analysis[@]}"; do
ignore+="--ignore \\$i "
done
@@ -3475,7 +3537,7 @@ fi
if [[ -n "\\$par_ignore_samples" ]]; then
ignore_samples=""
IFS="," read -ra ign_samples <<< \\$par_ignore_samples
IFS=";" read -ra ign_samples <<< \\$par_ignore_samples
for i in "\\${ign_samples[@]}"; do
ignore_samples+="--ignore-samples \\$i"
done
@@ -3618,7 +3680,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
val = val.join(par.multiple_sep)
}
if (par.direction == "output" && par.type == "file") {
val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
val = val
.replaceAll('\\$id', id)
.replaceAll('\\$\\{id\\}', id)
.replaceAll('\\$key', key)
.replaceAll('\\$\\{key\\}', key)
}
[parName, val]
}
@@ -3749,7 +3815,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def createParentStr = meta.config.allArguments
.findAll { it.type == "file" && it.direction == "output" && it.create_parent }
.collect { par ->
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
"\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
}
.join("\n")
@@ -3757,8 +3824,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def inputFileExports = meta.config.allArguments
.findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
.collect { par ->
def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
"\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
}
// NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3795,6 +3862,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
def procStr =
"""nextflow.enable.dsl=2
|
|def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
|process $procKey {$drctvStrs
|input:
| tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3806,10 +3874,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
|$stub
|\"\"\"
|script:$assertStr
|def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
|def parInject = args
| .findAll{key, value -> value != null}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
| .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
| .join("\\n")
|\"\"\"
|# meta exports
@@ -3894,7 +3961,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/multiqc",
"tag" : "v0.1.0"
"tag" : "0.2.0"
},
"tag" : "$id"
}'''),

3
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow.config → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config
View File

@@ -2,8 +2,9 @@ manifest {
name = 'multiqc'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = '0.2.0'
description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
author = 'Dorien Roosen'
}
process.container = 'nextflow/bash:latest'

20
target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json
View File

@@ -17,8 +17,8 @@
"input": {
"type":
"string",
"description": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report",
"help_text": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report.\n"
"description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report",
"help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n"
}
@@ -80,8 +80,8 @@
"include_modules": {
"type":
"string",
"description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module",
"help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module"
"description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module",
"help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module"
}
@@ -90,8 +90,8 @@
"exclude_modules": {
"type":
"string",
"description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules",
"help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules"
"description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules",
"help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules"
}
@@ -100,8 +100,8 @@
"ignore_analysis": {
"type":
"string",
"description": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. ",
"help_text": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. "
"description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. "
}
@@ -110,8 +110,8 @@
"ignore_samples": {
"type":
"string",
"description": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. ",
"help_text": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. "
"description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. "
}

2
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,7 +141,7 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -470,9 +470,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/io/untar/.config.vsh.yaml
View File

@@ -148,7 +148,7 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

4
target/executable/io/untar/untar
View File

@@ -476,9 +476,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io untar"
LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -139,7 +139,7 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

2
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -2972,7 +2972,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {

2
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -133,7 +133,7 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

2
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -2965,7 +2965,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {

16
target/nextflow/demultiplex/.config.vsh.yaml
View File

@@ -93,22 +93,22 @@ dependencies:
repository:
type: "vsh"
repo: "biobox"
tag: "v0.1.0"
tag: "v0.2.0"
- name: "falco"
repository:
type: "vsh"
repo: "biobox"
tag: "v0.1.0"
tag: "v0.2.0"
- name: "multiqc"
repository:
type: "vsh"
repo: "biobox"
tag: "v0.1.0"
tag: "v0.2.0"
repositories:
- type: "vsh"
name: "bb"
repo: "biobox"
tag: "v0.1.0"
tag: "v0.2.0"
license: "MIT"
links:
repository: "https://github.com/viash-hub/demultiplex"
@@ -186,16 +186,16 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
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"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
package_config:
name: "demultiplex"
version: "main"

16
target/nextflow/demultiplex/main.nf
View File

@@ -2932,7 +2932,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "biobox",
"tag" : "v0.1.0"
"tag" : "v0.2.0"
}
},
{
@@ -2940,7 +2940,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "biobox",
"tag" : "v0.1.0"
"tag" : "v0.2.0"
}
},
{
@@ -2948,7 +2948,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "biobox",
"tag" : "v0.1.0"
"tag" : "v0.2.0"
}
}
],
@@ -2957,7 +2957,7 @@ meta = [
"type" : "vsh",
"name" : "bb",
"repo" : "biobox",
"tag" : "v0.1.0"
"tag" : "v0.2.0"
}
],
"license" : "MIT",
@@ -3049,7 +3049,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {
@@ -3095,9 +3095,9 @@ include { untar } from "${meta.resources_dir}/../../nextflow/io/untar/main.nf"
include { gather_fastqs_and_validate } from "${meta.resources_dir}/../../nextflow/dataflow/gather_fastqs_and_validate/main.nf"
include { interop_summary_to_csv } from "${meta.resources_dir}/../../nextflow/io/interop_summary_to_csv/main.nf"
include { combine_samples } from "${meta.resources_dir}/../../nextflow/dataflow/combine_samples/main.nf"
include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf"
include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf"
include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf"
include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf"
include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf"
include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"
// inner workflow
// user-provided Nextflow code

2
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,7 +141,7 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

2
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -2977,7 +2977,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {

2
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -148,7 +148,7 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"

2
target/nextflow/io/untar/main.nf
View File

@@ -2989,7 +2989,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {

1
test_resources
View File

@@ -1 +0,0 @@
/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz