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Build branch htrnaseq/main with version main to htrnaseq on branch main (03e7939)

Browse Source 
Build pipeline: viash-hub.htrnaseq.main-s7m5b

Source commit: 03e7939a9b

Source message: Add integration test for generating a single eset (#73)
This commit is contained in:
CI
2025-09-10 19:55:10 +00:00
parent 8a9db1b415
commit 4216c221ee
82 changed files with 484 additions and 359 deletions
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6
CHANGELOG.md
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@@ -6,12 +6,16 @@
## New features
* `runner`: add output results to state in order for the workflow to be used as subworkflow (PR #68).
* `runner`: add output results to state in order for the workflow to be used as subworkflow (PR #68, PR 70, PR #71).
## Bug fixes
* `runner`: disable `publishFilesProc` because this workflow handles publishing itself (PR #68).
## Minor changes
* Bump craftbox to v0.3.0 (PR #69).
# htrnaseq v0.10.0
## Breaking changes

2
src/utils/concatRuns/config.vsh.yaml
View File

@@ -35,7 +35,7 @@ repositories:
- name: cb
type: vsh
repo: craftbox
tag: v0.2.0
tag: v0.3.0
runners:
- type: nextflow

18
src/workflows/runner/config.vsh.yaml
View File

@@ -38,11 +38,6 @@ argument_groups:
type: integer
min: 1
default: 10
- name: "--run_params"
type: file
required: false
direction: output
default: params.yaml
- name: Metadata arguments
arguments:
- name: --id
@@ -65,7 +60,14 @@ argument_groups:
type: string
required: true
- name: Output arguments
description: |
Parameters that determine the structure of the output. These parameters are provided for internal use only
and their defaults should not be overwritten.
arguments:
- name: "--run_params"
type: file
direction: output
default: params.yaml
- name: "--star_output_dir"
type: file
direction: output
@@ -101,6 +103,12 @@ test_resources:
- type: nextflow_script
path: test.nf
entrypoint: test_wf
- type: nextflow_script
path: test.nf
entrypoint: test_wf_with_lanes
- type: nextflow_script
path: test.nf
entrypoint: test_wf_only_one_eset
dependencies:
- name: utils/listInputDir

8
src/workflows/runner/integration_test.sh
View File

@@ -22,3 +22,11 @@ nextflow \
-resume \
-profile docker,local
nextflow \
run . \
-main-script src/workflows/runner/test.nf \
-config ./src/config/labels.config \
-entry test_wf_only_one_eset \
-resume \
-profile docker,local

12
src/workflows/runner/main.nf
View File

@@ -68,7 +68,8 @@ workflow run_wf {
"star_qc_metrics_dir_workflow": state.star_qc_metrics_dir,
"eset_dir_workflow": state.eset_dir,
"f_data_dir_workflow": state.f_data_dir,
"p_data_dir_workflow": state.p_data_dir
"p_data_dir_workflow": state.p_data_dir,
"run_params_workflow": state.run_params,
]
return [id, new_state]
}
@@ -128,7 +129,7 @@ workflow run_wf {
umi_length: "umi_length",
sample_id: "sample_id",
],
toState: { id, result, state -> state + result }
toState: { id, result, state -> state + result.findAll{it.key != "run_params"} }
)
// The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
@@ -138,6 +139,7 @@ workflow run_wf {
results_publish_ch = htrnaseq_ch
| combine(save_params_ch)
| map {new_id, grouped_ch_state, save_params_id, save_params_state ->
assert save_params_state.run_params.isFile()
def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
return [new_id, new_state]
}
@@ -171,6 +173,7 @@ workflow run_wf {
"eset_dir_workflow",
"f_data_dir_workflow",
"p_data_dir_workflow",
"run_params_workflow",
"f_data",
"run_params"
]
@@ -215,8 +218,8 @@ workflow run_wf {
html_report: state.html_report,
run_params: state.run_params,
// Output locations
run_params_output: "${prefix}/${state.run_params.name}",
html_report_output: "${prefix}/${state.html_report.name}",
run_params_output: "${prefix}/${state.run_params_workflow}",
star_output_dir: "${prefix}/${state.star_output_dir_workflow}",
nrReadsNrGenesPerChrom_dir: "${prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
star_qc_metrics_dir: "${prefix}/${state.star_qc_metrics_dir_workflow}",
@@ -225,7 +228,7 @@ workflow run_wf {
p_data_dir: "${prefix}/${state.p_data_dir_workflow}"
]
},
toState: { id, result, state -> result },
toState: { id, result, state -> result + ["run_params": state.run_params] },
directives: [
publishDir: [
path: "${params.results_publish_dir}",
@@ -241,6 +244,7 @@ workflow run_wf {
"eset_dir",
"f_data_dir",
"p_data_dir",
"run_params",
]
)

111
src/workflows/runner/test.nf
View File

@@ -111,6 +111,7 @@ workflow test_wf {
}
assert output_state.star_qc_metrics_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
assert output_state.nrReadsNrGenesPerChrom_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
assert output_state.run_params.isFile()
}
@@ -327,4 +328,114 @@ workflow test_wf_with_lanes {
throw new WorkflowScriptErrorException("Integration test failed!", e)
}
}
}
workflow test_wf_only_one_eset {
pipeline_version = get_version(viash_config)
resources_test = file(params.resources_test)
// results_publish_dir and results_publish_dir are inherited using params
// but they must be defined in the state as well because viash will check
// if all arguments are present in the hashmap
output_ch = Channel.fromList([
[
id: "run_1",
input: resources_test.resolve("10k_with_lanes/SRR14730301"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
],
])
| map { state -> [state.id, state]}
| runner.run(
toState: { id, output, state -> output + [orig_input: state.input] }
)
| view { output ->
assert output.size() == 2 : "outputs should contain two elements; [id, file]"
"Output: $output"
}
tosortedlistch = output_ch
| toSortedList()
| map {events ->
assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
}
workflow.onComplete = {
try {
// Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
// So in order for the assert statement to work (or allow other errors to let the tests to fail)
// We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
// The error message will show up in .nextflow.log
def fastq_subdir = file("${params.fastq_publish_dir}")
assert fastq_subdir.isDirectory()
def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
def expected_run_folders = ["run_1"].toSet()
assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
unique_dirs = [
"run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
]
assert unique_dirs.every{it.value.size() == 1}
unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
assert unique_dirs.every{it.value.isDirectory()}
assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
def expected_samples = [
"run1": "VH02001612",
]
unique_dirs.each{_key, _value ->
def expected_sample = expected_samples[_key]
def expected_sample_dir = _value.resolve(expected_sample)
assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
def expected_fastq_files = [
"A1_R1_001.fastq", "A1_R2_001.fastq",
"B1_R1_001.fastq", "B1_R2_001.fastq",
"unknown_R1_001.fastq", "unknown_R2_001.fastq"]
def found_files = files("${expected_sample_dir}/*.fastq", type: 'any')
assert found_files.every{it.isFile()}
assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
}
def results_subdir = file("${params.results_publish_dir}")
assert fastq_subdir.isDirectory()
def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
assert expected_subdir.isDirectory()
def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
assert expected_result_dir.size() == 1
expected_result_dir = expected_result_dir[0]
assert expected_result_dir.isDirectory()
def expected_esets = ["VH02001612.rds"]
def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
assert found_esets.size() == 1
assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
expected_table_filenames = ["VH02001612.txt"]
def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
assert found_pdata.size() == 1
assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
assert found_nr_genes_nr_reads.size() == 1
assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
assert found_star_logs.size() == 1
assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
def star_output = file("${expected_result_dir}/star_output", type: 'any')
assert star_output.isDirectory()
assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612"].toSet()
assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
assert file("${expected_result_dir}/report.html").isFile()
assert file("${expected_result_dir}/params.yaml").isFile()
assert file("${expected_result_dir}/fData/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
} catch (Exception e) {
throw new WorkflowScriptErrorException("Integration test failed!", e)
}
}
}

2
src/workflows/well_demultiplex/config.vsh.yaml
View File

@@ -71,7 +71,7 @@ repositories:
- name: cb
type: vsh
repo: craftbox
tag: v0.2.0
tag: v0.3.0
runners:
- type: nextflow

106
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/nextflow_schema.json
View File

@@ -1,106 +0,0 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "concat_text",
"description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
"type": "object",
"definitions": {
"input arguments" : {
"title": "Input arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files",
"help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files."
}
}
},
"output arguments" : {
"title": "Output arguments",
"type": "object",
"description": "No description",
"properties": {
"gzip_output": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
"help_text": "Type: `boolean_true`, default: `false`. Should the output be zipped?"
,
"default":false
}
,
"output": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped",
"help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped."
,
"default":"$id.$key.output.txt"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input arguments"
},
{
"$ref": "#/definitions/output arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

81
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/nextflow_schema.json
View File

@@ -1,81 +0,0 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "move_files_to_directory",
"description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\u0027t exist.",
"type": "object",
"definitions": {
"arguments" : {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory",
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory."
}
,
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output`. Path to output directory",
"help_text": "Type: `file`, required, default: `$id.$key.output`. Path to output directory"
,
"default":"$id.$key.output"
}
}
},
"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/arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

12
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/.config.vsh.yaml → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "concat_text"
version: "v0.2.0"
version: "v0.3.0"
authors:
- name: "Toni Verbeiren"
roles:
@@ -156,7 +156,7 @@ engines:
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apk"
@@ -175,12 +175,12 @@ build_info:
output: "target/nextflow/concat_text"
executable: "target/nextflow/concat_text/main.nf"
viash_version: "0.9.4"
git_commit: "1c1b0a4a1aff891ab678072b0ba915ac3ac71610"
git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-8-g1c1b0a4"
git_tag: "v0.1.0-11-ga1801c5"
package_config:
name: "craftbox"
version: "v0.2.0"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -203,7 +203,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"

16
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/main.nf
View File

@@ -1,4 +1,4 @@
// concat_text v0.2.0
// concat_text v0.3.0
//
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "concat_text",
"version" : "v0.2.0",
"version" : "v0.3.0",
"authors" : [
{
"name" : "Toni Verbeiren",
@@ -3238,7 +3238,7 @@ meta = [
"id" : "docker",
"image" : "alpine:latest",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "v0.3.0",
"namespace_separator" : "/",
"setup" : [
{
@@ -3262,13 +3262,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/concat_text",
"viash_version" : "0.9.4",
"git_commit" : "1c1b0a4a1aff891ab678072b0ba915ac3ac71610",
"git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
"git_remote" : "https://github.com/viash-hub/craftbox",
"git_tag" : "v0.1.0-8-g1c1b0a4"
"git_tag" : "v0.1.0-11-ga1801c5"
},
"package_config" : {
"name" : "craftbox",
"version" : "v0.2.0",
"version" : "v0.3.0",
"summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
"description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear documentation for components and their parameters.\n * Full exposure of underlying script/tool arguments for fine-grained control.\n * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n * Unit tested where applicable to ensure components function as expected.\n",
"viash_version" : "0.9.4",
@@ -3278,7 +3278,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'v0.3.0'"
],
"keywords" : [
"scripts",
@@ -3746,7 +3746,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/craftbox/concat_text",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/nextflow.config → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'concat_text'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'v0.3.0'
description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
author = 'Toni Verbeiren, Dries Schaumont'
}

68
target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/nextflow_schema.json Normal file
View File

@@ -0,0 +1,68 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"title": "concat_text",
"description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
"type": "object",
"$defs": {
"input arguments": {
"title": "Input arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type": "array",
"items": {
"type": "string"
},
"format": "path",
"exists": true,
"description": "A list of (gzipped) text files.",
"help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input?.txt.gz\"]`. "
}
}
},
"output arguments": {
"title": "Output arguments",
"type": "object",
"description": "No description",
"properties": {
"gzip_output": {
"type": "boolean",
"description": "Should the output be zipped?",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
},
"output": {
"type": "string",
"format": "path",
"description": "File to write the output to, optionally gzipped.",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
"default": "$id.$key.output.txt"
}
}
},
"nextflow input-output arguments": {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type": "string",
"description": "Path to an output directory.",
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input arguments"
},
{
"$ref": "#/$defs/output arguments"
},
{
"$ref": "#/$defs/nextflow input-output arguments"
}
]
}

19
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/.config.vsh.yaml → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "move_files_to_directory"
version: "v0.2.0"
version: "v0.3.0"
authors:
- name: "Dorien Roosen"
roles:
@@ -36,6 +36,13 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--keep_symbolic_links"
alternatives:
- "-d"
description: "Preserve symbolic links."
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
@@ -128,7 +135,7 @@ engines:
id: "docker"
image: "debian:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apt"
@@ -146,12 +153,12 @@ build_info:
output: "target/nextflow/move_files_to_directory"
executable: "target/nextflow/move_files_to_directory/main.nf"
viash_version: "0.9.4"
git_commit: "1c1b0a4a1aff891ab678072b0ba915ac3ac71610"
git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-8-g1c1b0a4"
git_tag: "v0.1.0-11-ga1801c5"
package_config:
name: "craftbox"
version: "v0.2.0"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -174,7 +181,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"

35
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/main.nf → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory/main.nf
View File

@@ -1,4 +1,4 @@
// move_files_to_directory v0.2.0
// move_files_to_directory v0.3.0
//
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3034,7 +3034,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "move_files_to_directory",
"version" : "v0.2.0",
"version" : "v0.3.0",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3082,6 +3082,15 @@ meta = [
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "boolean_true",
"name" : "--keep_symbolic_links",
"alternatives" : [
"-d"
],
"description" : "Preserve symbolic links.",
"direction" : "input"
}
]
}
@@ -3196,7 +3205,7 @@ meta = [
"id" : "docker",
"image" : "debian:latest",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "v0.3.0",
"namespace_separator" : "/",
"setup" : [
{
@@ -3219,13 +3228,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/move_files_to_directory",
"viash_version" : "0.9.4",
"git_commit" : "1c1b0a4a1aff891ab678072b0ba915ac3ac71610",
"git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
"git_remote" : "https://github.com/viash-hub/craftbox",
"git_tag" : "v0.1.0-8-g1c1b0a4"
"git_tag" : "v0.1.0-11-ga1801c5"
},
"package_config" : {
"name" : "craftbox",
"version" : "v0.2.0",
"version" : "v0.3.0",
"summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
"description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear documentation for components and their parameters.\n * Full exposure of underlying script/tool arguments for fine-grained control.\n * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n * Unit tested where applicable to ensure components function as expected.\n",
"viash_version" : "0.9.4",
@@ -3235,7 +3244,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'v0.3.0'"
],
"keywords" : [
"scripts",
@@ -3270,6 +3279,7 @@ set -eo pipefail
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_KEEP_SYMBOLIC_LINKS+x} ]; then echo "${VIASH_PAR_KEEP_SYMBOLIC_LINKS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_keep_symbolic_links='&'#" ; else echo "# par_keep_symbolic_links="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -3296,12 +3306,19 @@ if [[ ! -d "\\$par_output" ]]; then
mkdir -p "\\$par_output"
fi
extra_params=( )
if [ "\\$par_keep_symbolic_links" == "true" ]; then
extra_params+=( "-d" )
fi
# Process multiple input files
IFS=";" read -ra input_files <<< "\\$par_input"
for file in "\\${input_files[@]}"; do
# Check if the file exists before copying
if [[ -f "\\$file" ]]; then
cp "\\$file" "\\$par_output/"
cp \\${extra_params[@]} "\\$file" "\\$par_output/"
echo "Copied \\$file to \\$par_output/"
else
echo "Warning: Input file \\$file does not exist, skipping"
@@ -3689,7 +3706,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/craftbox/move_files_to_directory",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/nextflow.config → target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'move_files_to_directory'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'v0.3.0'
description = 'This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\'t exist.'
author = 'Dorien Roosen'
}

58
target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory/nextflow_schema.json Normal file
View File

@@ -0,0 +1,58 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"title": "move_files_to_directory",
"description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.",
"type": "object",
"$defs": {
"arguments": {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type": "array",
"items": {
"type": "string"
},
"format": "path",
"exists": true,
"description": "Paths of the files that will be copied into the output directory.",
"help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
},
"output": {
"type": "string",
"format": "path",
"description": "Path to output directory",
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
"default": "$id.$key.output"
},
"keep_symbolic_links": {
"type": "boolean",
"description": "Preserve symbolic links.",
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
"default": false
}
}
},
"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": "Path to an output directory.",
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/arguments"
},
{
"$ref": "#/$defs/nextflow input-output arguments"
}
]
}

2
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -206,7 +206,7 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/eset/create_eset/create_eset
View File

@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,7 +183,7 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/eset/create_fdata/create_fdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,7 +197,7 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/eset/create_pdata/create_pdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,7 +155,7 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/integration_test_components/htrnaseq/check_eset/check_eset
View File

@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,7 +164,7 @@ build_info:
output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -139,7 +139,7 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/io/publish_fastqs/publish_fastqs
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -279,7 +279,7 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/io/publish_results/publish_results
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
LABEL org.opencontainers.image.created="2025-09-02T13:10:27Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -285,7 +285,7 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/parallel_map/parallel_map
View File

@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
COPY STAR /usr/local/bin/$STAR_BINARY
LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -215,7 +215,7 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/report/create_report/create_report
View File

@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component report create_report"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,7 +204,7 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/stats/combine_star_logs/combine_star_logs
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,7 +188,7 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -260,7 +260,7 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -151,7 +151,7 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/utils/save_params/save_params
View File

@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "pyyaml"
LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
LABEL org.opencontainers.image.created="2025-09-02T13:10:26Z"
LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -206,7 +206,7 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_eset/main.nf
View File

@@ -3309,7 +3309,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,7 +183,7 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3279,7 +3279,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,7 +197,7 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3293,7 +3293,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,7 +155,7 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3233,7 +3233,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,7 +164,7 @@ build_info:
output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3244,7 +3244,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -139,7 +139,7 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3207,7 +3207,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -279,7 +279,7 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3369,7 +3369,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -285,7 +285,7 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/parallel_map/main.nf
View File

@@ -3379,7 +3379,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -215,7 +215,7 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/report/create_report/main.nf
View File

@@ -3323,7 +3323,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,7 +204,7 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3295,7 +3295,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,7 +188,7 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3279,7 +3279,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -260,7 +260,7 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3361,7 +3361,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

8
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -75,12 +75,12 @@ dependencies:
repository:
type: "vsh"
repo: "craftbox"
tag: "v0.2.0"
tag: "v0.3.0"
repositories:
- type: "vsh"
name: "cb"
repo: "craftbox"
tag: "v0.2.0"
tag: "v0.3.0"
license: "MIT"
links:
repository: "https://github.com/viash-hub/htrnaseq"
@@ -160,10 +160,10 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
- "target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text"
package_config:
name: "htrnaseq"
version: "main"

8
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3125,7 +3125,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "craftbox",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
}
}
],
@@ -3134,7 +3134,7 @@ meta = [
"type" : "vsh",
"name" : "cb",
"repo" : "craftbox",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
}
],
"license" : "MIT",
@@ -3229,7 +3229,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3276,7 +3276,7 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/main.nf"
// inner workflow
// user-provided Nextflow code

2
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -169,7 +169,7 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3236,7 +3236,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/utils/save_params/.config.vsh.yaml
View File

@@ -151,7 +151,7 @@ build_info:
output: "target/nextflow/utils/save_params"
executable: "target/nextflow/utils/save_params/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/utils/save_params/main.nf
View File

@@ -3223,7 +3223,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/utils/save_params",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -345,7 +345,7 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"

2
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3484,7 +3484,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

34
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -68,17 +68,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--run_params"
info: null
default:
- "params.yaml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Metadata arguments"
arguments:
- type: "string"
@@ -122,7 +111,20 @@ argument_groups:
multiple: false
multiple_sep: ";"
- name: "Output arguments"
description: "Parameters that determine the structure of the output. These parameters\
\ are provided for internal use only\nand their defaults should not be overwritten.\n"
arguments:
- type: "file"
name: "--run_params"
info: null
default:
- "params.yaml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--star_output_dir"
info: null
@@ -208,6 +210,14 @@ test_resources:
path: "test.nf"
is_executable: true
entrypoint: "test_wf"
- type: "nextflow_script"
path: "test.nf"
is_executable: true
entrypoint: "test_wf_with_lanes"
- type: "nextflow_script"
path: "test.nf"
is_executable: true
entrypoint: "test_wf_only_one_eset"
info: null
status: "enabled"
scope:
@@ -312,7 +322,7 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/utils/listInputDir"

53
target/nextflow/workflows/runner/main.nf
View File

@@ -3099,19 +3099,6 @@ meta = [
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--run_params",
"default" : [
"params.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
}
]
},
@@ -3170,7 +3157,21 @@ meta = [
},
{
"name" : "Output arguments",
"description" : "Parameters that determine the structure of the output. These parameters are provided for internal use only\nand their defaults should not be overwritten.\n",
"arguments" : [
{
"type" : "file",
"name" : "--run_params",
"default" : [
"params.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--star_output_dir",
@@ -3281,6 +3282,18 @@ meta = [
"path" : "test.nf",
"is_executable" : true,
"entrypoint" : "test_wf"
},
{
"type" : "nextflow_script",
"path" : "test.nf",
"is_executable" : true,
"entrypoint" : "test_wf_with_lanes"
},
{
"type" : "nextflow_script",
"path" : "test.nf",
"is_executable" : true,
"entrypoint" : "test_wf_only_one_eset"
}
],
"status" : "enabled",
@@ -3418,7 +3431,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3543,7 +3556,8 @@ workflow run_wf {
"star_qc_metrics_dir_workflow": state.star_qc_metrics_dir,
"eset_dir_workflow": state.eset_dir,
"f_data_dir_workflow": state.f_data_dir,
"p_data_dir_workflow": state.p_data_dir
"p_data_dir_workflow": state.p_data_dir,
"run_params_workflow": state.run_params,
]
return [id, new_state]
}
@@ -3603,7 +3617,7 @@ workflow run_wf {
umi_length: "umi_length",
sample_id: "sample_id",
],
toState: { id, result, state -> state + result }
toState: { id, result, state -> state + result.findAll{it.key != "run_params"} }
)
// The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
@@ -3613,6 +3627,7 @@ workflow run_wf {
results_publish_ch = htrnaseq_ch
| combine(save_params_ch)
| map {new_id, grouped_ch_state, save_params_id, save_params_state ->
assert save_params_state.run_params.isFile()
def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
return [new_id, new_state]
}
@@ -3646,6 +3661,7 @@ workflow run_wf {
"eset_dir_workflow",
"f_data_dir_workflow",
"p_data_dir_workflow",
"run_params_workflow",
"f_data",
"run_params"
]
@@ -3690,8 +3706,8 @@ workflow run_wf {
html_report: state.html_report,
run_params: state.run_params,
// Output locations
run_params_output: "${prefix}/${state.run_params.name}",
html_report_output: "${prefix}/${state.html_report.name}",
run_params_output: "${prefix}/${state.run_params_workflow}",
star_output_dir: "${prefix}/${state.star_output_dir_workflow}",
nrReadsNrGenesPerChrom_dir: "${prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}",
star_qc_metrics_dir: "${prefix}/${state.star_qc_metrics_dir_workflow}",
@@ -3700,7 +3716,7 @@ workflow run_wf {
p_data_dir: "${prefix}/${state.p_data_dir_workflow}"
]
},
toState: { id, result, state -> result },
toState: { id, result, state -> result + ["run_params": state.run_params] },
directives: [
publishDir: [
path: "${params.results_publish_dir}",
@@ -3716,6 +3732,7 @@ workflow run_wf {
"eset_dir",
"f_data_dir",
"p_data_dir",
"run_params",
]
)

16
target/nextflow/workflows/runner/nextflow_schema.json
View File

@@ -50,13 +50,6 @@
"description": "Length of the UMI sequences\n",
"help_text": "Type: `integer`, multiple: `False`, default: `10`. ",
"default": 10
},
"run_params": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"params.yaml\"`, direction: `output`. ",
"default": "params.yaml"
}
}
},
@@ -102,8 +95,15 @@
"output arguments": {
"title": "Output arguments",
"type": "object",
"description": "No description",
"description": "Parameters that determine the structure of the output. These parameters are provided for internal use only\nand their defaults should not be overwritten.\n",
"properties": {
"run_params": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"params.yaml\"`, direction: `output`. ",
"default": "params.yaml"
},
"star_output_dir": {
"type": "string",
"format": "path",

12
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -128,12 +128,12 @@ dependencies:
repository:
type: "vsh"
repo: "craftbox"
tag: "v0.2.0"
tag: "v0.3.0"
- name: "move_files_to_directory"
repository:
type: "vsh"
repo: "craftbox"
tag: "v0.2.0"
tag: "v0.3.0"
repositories:
- type: "vsh"
name: "bb"
@@ -142,7 +142,7 @@ repositories:
- type: "vsh"
name: "cb"
repo: "craftbox"
tag: "v0.2.0"
tag: "v0.3.0"
license: "MIT"
links:
repository: "https://github.com/viash-hub/htrnaseq"
@@ -222,12 +222,12 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory"
- "target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text"
- "target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory"
package_config:
name: "htrnaseq"
version: "main"

12
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3209,7 +3209,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "craftbox",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
}
},
{
@@ -3217,7 +3217,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "craftbox",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
}
}
],
@@ -3232,7 +3232,7 @@ meta = [
"type" : "vsh",
"name" : "cb",
"repo" : "craftbox",
"tag" : "v0.2.0"
"tag" : "v0.3.0"
}
],
"license" : "MIT",
@@ -3327,7 +3327,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3375,8 +3375,8 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { cutadapt } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt/main.nf"
include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
include { move_files_to_directory } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/main.nf"
include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text/main.nf"
include { move_files_to_directory } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/move_files_to_directory/main.nf"
// inner workflow
// user-provided Nextflow code

2
target/nextflow/workflows/well_metadata/.config.vsh.yaml
View File

@@ -215,7 +215,7 @@ build_info:
output: "target/nextflow/workflows/well_metadata"
executable: "target/nextflow/workflows/well_metadata/main.nf"
viash_version: "0.9.4"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/well_metadata/main.nf
View File

@@ -3299,7 +3299,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_metadata",
"viash_version" : "0.9.4",
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {