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Build branch htrnaseq/main with version main to htrnaseq on branch main (92755e8)

Browse Source 
Build pipeline: viash-hub.htrnaseq.main-666pl

Source commit: 92755e84e7

Source message: Runner: output state and rework publishing (#68)

* add eset output param

* add outputs to publishing and runner

* update publishing

* Update publishing

* Remove debug statements

* Undo change to integration test script

* Add asserts

* Fix asserts and canonicalization of publish paths

* Move fData to folder

* Add CHANGELOG entry [ci skip]

---------

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
This commit is contained in:
CI
2025-09-02 08:17:05 +00:00
parent b51996294b
commit f683dfcf8e
111 changed files with 1549 additions and 573 deletions
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1
.gitignore vendored
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@@ -1,5 +1,6 @@
target
testData
resources_test
# Nextflow related files
.nextflow

14
CHANGELOG.md
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@@ -1,3 +1,17 @@
# htrnaseq v0.11.0
## Breaking changes
* `runner`: feature annotation data (fData) is now output to a subfolder `fData` (PR #68).
## New features
* `runner`: add output results to state in order for the workflow to be used as subworkflow (PR #68).
## Bug fixes
* `runner`: disable `publishFilesProc` because this workflow handles publishing itself (PR #68).
# htrnaseq v0.10.0
## Breaking changes

45
_viash.yaml
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@@ -1,56 +1,21 @@
name: htrnaseq
summary: |
A workflow for high-throughput RNA-seq data analyses.
description: |
This workflow is designed to process high-throughput RNA-seq data, where every
well of a microarray plate is a sample. A fasta file provided as input
defines the mapping between sample barcodes and wells.
The workflow is built in a modular fashion, where most of the base functionality
is provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)
supplemented by custom base components and workflow components in this package.
The full workflow is split in two major subworkflows that can be run independently:
* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.
* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.
Each of those can be started individually, or the full workflow can be run in two ways:
1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq)
containing the main functionality.
2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a
number of choices (input/output structure and location) have been made.
Input for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running
[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.
description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
license: MIT
keywords:
[
bioinformatics,
sequencing,
high-throughput,
RNAseq,
mapping,
counting,
pipeline,
workflow,
]
keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
links:
issue_tracker: https://github.com/viash-hub/htrnaseq/issues
repository: https://github.com/viash-hub/htrnaseq
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main
organization: vsh

89
src/io/publish_results/code.sh
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@@ -1,44 +1,93 @@
#!/bin/bash
echo "Publishing $par_input -> $par_output"
set -eo pipefail
echo "Publishing results to multiple output directories"
# Create output directories for multiple files
echo "Creating output directories..."
path_pars=(
par_star_output_dir
par_nrReadsNrGenesPerChrom_dir
par_star_qc_metrics_dir
par_eset_dir
par_f_data_dir
par_p_data_dir
par_html_report_output
par_run_params_output
)
for par in ${path_pars[@]}; do
curr_val="${!par}"
new_value=$(realpath --canonicalize-missing "$curr_val")
declare -g "$par=$new_value"
done
mkdir -p "$par_star_output_dir" && echo "$par_star_output_dir created"
mkdir -p "$par_nrReadsNrGenesPerChrom_dir" && echo "$par_nrReadsNrGenesPerChrom_dir created"
mkdir -p "$par_star_qc_metrics_dir" && echo "$par_star_qc_metrics_dir created"
mkdir -p "$par_eset_dir" && echo "$par_eset_dir created"
mkdir -p "$par_f_data_dir" && echo "$par_f_data_dir created"
mkdir -p "$par_p_data_dir" && echo "$par_p_data_dir created"
echo
echo "Creating directory if it does not exist:"
mkdir -p "$par_output" && echo "$par_output created"
echo
echo "Copying files..."
echo "Copying STAR output files..."
IFS=";" read -ra star_output <<<$par_star_output
IFS=";" read -ra nrReadsNrGenesPerChrom <<<$par_nrReadsNrGenesPerChrom
IFS=";" read -ra star_qc_metrics <<<$par_star_qc_metrics
IFS=";" read -ra eset <<<$par_eset
IFS=";" read -ra f_data <<<$par_f_data
IFS=";" read -ra p_data <<<$par_p_data
for i in "${star_output[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_star_output_dir/"
cp -rL "$i" "$par_star_output_dir/"
done
echo
echo "Copying nrReadsNrGenesPerChrom files..."
IFS=";" read -ra nrReadsNrGenesPerChrom <<<$par_nrReadsNrGenesPerChrom
for i in "${nrReadsNrGenesPerChrom[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_nrReadsNrGenesPerChrom_dir/"
cp -rL "$i" "$par_nrReadsNrGenesPerChrom_dir/"
done
echo
echo "Copying STAR QC metrics files..."
IFS=";" read -ra star_qc_metrics <<<$par_star_qc_metrics
for i in "${star_qc_metrics[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_star_qc_metrics_dir/"
cp -rL "$i" "$par_star_qc_metrics_dir/"
done
echo
echo "Copying eset files..."
IFS=";" read -ra eset <<<$par_eset
for i in "${eset[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_eset_dir/"
cp -rL "$i" "$par_eset_dir/"
done
echo
echo "Copying f_data files..."
IFS=";" read -ra f_data <<<$par_f_data
for i in "${f_data[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_f_data_dir/"
cp -rL "$i" "$par_f_data_dir/"
done
echo
echo "Copying p_data files..."
IFS=";" read -ra p_data <<<$par_p_data
for i in "${p_data[@]}"; do
cp -rL "$i" "$par_output/"
echo "Copying $i to $par_p_data_dir/"
cp -rL "$i" "$par_p_data_dir/"
done
cp -rL "$par_html_report" "$par_output/"
echo
echo "Copying single files directly..."
mkdir -p $(dirname "$par_html_report_output")
echo "Copying $par_html_report to $par_html_report_output"
cp -L "$par_html_report" "$par_html_report_output"
cp -rL "$par_run_params" "$par_output/"
echo "Copying $par_run_params to $par_run_params_output"
mkdir -p $(dirname "$par_run_params_output")
cp -L "$par_run_params" "$par_run_params_output"
echo
echo "Publishing completed successfully!"

39
src/io/publish_results/config.vsh.yaml
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@@ -35,13 +35,44 @@ argument_groups:
- name: "--run_params"
type: file
required: true
- name: Output arguments
- name: Output directory
description: |
Determines the name of output directories
arguments:
- name: --output
- name: --star_output_dir
type: file
direction: output
# ID is the well barcode
default: "$id/"
default: "star_output"
- name: --nrReadsNrGenesPerChrom_dir
type: file
direction: output
default: "nrReadsNrGenesPerChrom"
- name: --star_qc_metrics_dir
type: file
direction: output
default: "starLogs"
- name: --eset_dir
type: file
direction: output
default: "esets"
- name: --f_data_dir
type: file
direction: output
default: "fData"
- name: --p_data_dir
type: file
direction: output
default: "pData"
- name: "Output file arguments"
description: Determines the name of output files
arguments:
- name: "--run_params_output"
type: file
direction: output
- name: "--html_report_output"
type: file
direction: output
resources:
- type: bash_script

1
src/workflows/htrnaseq/main.nf
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@@ -344,7 +344,6 @@ workflow run_wf {
| setState([
"star_output": "star_output",
"fastq_output": "fastq_output_directory",
"star_output": "star_output",
"nrReadsNrGenesPerChrom": "nrReadsNrGenesPerChromPool",
"star_qc_metrics": "star_qc_metrics",
"eset": "eset",

30
src/workflows/runner/config.vsh.yaml
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@@ -64,11 +64,38 @@ argument_groups:
- name: --results_publish_dir
type: string
required: true
- name: Output arguments
arguments:
- name: "--star_output_dir"
type: file
direction: output
default: "star_output"
- name: "--nrReadsNrGenesPerChrom_dir"
type: file
direction: output
default: "nrReadsNrGenesPerChrom"
- name: "--star_qc_metrics_dir"
type: file
direction: output
default: "starLogs"
- name: "--eset_dir"
type: file
direction: output
default: "esets"
- name: "--f_data_dir"
type: file
direction: output
default: "fData"
- name: "--p_data_dir"
type: file
direction: output
default: "pData"
resources:
- type: nextflow_script
path: main.nf
entrypoint: run_wf
- path: disable_publishfiles_process.config
test_resources:
- type: nextflow_script
@@ -89,6 +116,9 @@ dependencies:
runners:
- type: nextflow
config:
script:
- includeConfig("disable_publishfiles_process.config")
engines:
- type: native

5
src/workflows/runner/disable_publishfiles_process.config Normal file
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@@ -0,0 +1,5 @@
process {
withName: publishFilesProc {
publishDir = [ enabled: false ]
}
}

2
src/workflows/runner/integration_test.sh
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@@ -1,6 +1,8 @@
# get the root of the directory
REPO_ROOT=$(git rev-parse --show-toplevel)
set -eo pipefail
# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

203
src/workflows/runner/main.nf
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@@ -26,7 +26,6 @@ workflow run_wf {
def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states]
return [new_id, new_state]
}
| save_params.run(
key: "save_params_runner",
fromState: {id, state ->
@@ -60,6 +59,19 @@ workflow run_wf {
)
htrnaseq_ch = input_ch
| map { id, state ->
// The argument names for this workflow and the htrnaseq workflow may overlap
// here, we store a copy in order to make sure to not accidentally overwrite the state.
def new_state = state + [
"star_output_dir_workflow": state.star_output_dir,
"nrReadsNrGenesPerChrom_dir_workflow": state.nrReadsNrGenesPerChrom_dir,
"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
]
return [id, new_state]
}
| listInputDir.run(
fromState: [
"input": "input",
@@ -122,46 +134,78 @@ workflow run_wf {
// The HT-RNAseq workflow outputs multiple events, one per 'pool' (usually a plate)
// but for publishing the results, this is not handy because we want to use the $id
// variable as a pointer to the target data.
//
// So, we should combine everything together
//
// project_id / experiment_id / "data_processed" / date_workflow
grouped_ch = htrnaseq_ch
| toSortedList
| map{ vs ->
def all_fastqs
[
vs[0][1].run_id, // The original ID
[
star_output: reduce_paths(vs.collect{ it[1].star_output }.flatten()),
nrReadsNrGenesPerChrom: reduce_paths(vs.collect{ it[1].nrReadsNrGenesPerChrom }),
star_qc_metrics: reduce_paths(vs.collect{ it[1].star_qc_metrics }),
eset: reduce_paths(vs.collect{ it[1].eset }),
f_data: reduce_paths(vs.collect{ it[1].f_data }),
p_data: reduce_paths(vs.collect{ it[1].p_data }),
fastq_output: vs.collect{ it[1].fastq_output }.flatten().unique(),
html_report: vs.collect{ it[1].html_report }[0], // The report is for all pools
plain_output: vs.collect{ it[1].plain_output }[0],
project_id: vs.collect{ it[1].project_id }[0],
experiment_id: vs.collect{ it[1].experiment_id }[0]
]
]
}
grouped_with_params_list_ch = grouped_ch.combine(save_params_ch)
results_publish_ch = htrnaseq_ch
| combine(save_params_ch)
| map {new_id, grouped_ch_state, save_params_id, save_params_state ->
def new_state = grouped_ch_state + ["run_params": save_params_state.run_params]
return [new_id, new_state]
}
| toSortedList
| map{ vs ->
def states = vs.collect{it[1]}
// The STAR output is a directory for each well in a plate (or pool of plates).
// The wells are grouped into a directory per sample. The name of this directory should
// match the sample_id.
def star_output_samples = states.collectMany{state ->
state.star_output.collect{
def star_sample_dir = it.parent
assert star_sample_dir.name == state.sample_id: "Unexpected state: the parent directory of STAR output \
path '${it}' should match with the sample ID ${sample_id}"
star_sample_dir
}
}
def new_state = [
"star_output": star_output_samples,
]
// Keys for which the values should be the same across samples
def state_keys_unique = [
"html_report",
"project_id",
"experiment_id",
"star_output_dir_workflow",
"nrReadsNrGenesPerChrom_dir_workflow",
"star_qc_metrics_dir_workflow",
"eset_dir_workflow",
"f_data_dir_workflow",
"p_data_dir_workflow",
"f_data",
"run_params"
]
def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name ->
argument_values = states.collect{it.get(argument_name)}.unique()
assert argument_values.size() == 1, "State error: values for argument $argument_name should be the same across states. \
Argument values: $argument_values"
// take the unique value from the set (there is only one)
def argument_value
argument_values.each { argument_value = it }
state_to_update + [(argument_name): argument_value]
}
results_publish_ch = grouped_with_params_list_ch
// Keys that just require gathering of values across samples
def state_keys_collect = [
"nrReadsNrGenesPerChrom",
"star_qc_metrics",
"eset",
"p_data",
]
def state_collect = state_keys_collect.collectEntries{ key_ ->
[key_, states.collect{it.get(key_)}]
}
new_state = new_state + state_unique_keys + state_collect
[states[0].run_id, new_state]
}
| publish_results.run(
fromState: { id, state ->
def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
println("Publising results to ${params.results_publish_dir}/${output_dir}")
def prefix = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
println("Publising results to ${params.results_publish_dir}/${prefix}")
[
// Inputs
star_output: state.star_output,
nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
star_qc_metrics: state.star_qc_metrics,
@@ -170,10 +214,18 @@ workflow run_wf {
p_data: state.p_data,
html_report: state.html_report,
run_params: state.run_params,
output: output_dir.toString()
// Output locations
run_params_output: "${prefix}/${state.run_params.name}",
html_report_output: "${prefix}/${state.html_report.name}",
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}",
eset_dir: "${prefix}/${state.eset_dir_workflow}",
f_data_dir: "${prefix}/${state.f_data_dir_workflow}",
p_data_dir: "${prefix}/${state.p_data_dir_workflow}"
]
},
toState: { id, result, state -> state },
toState: { id, result, state -> result },
directives: [
publishDir: [
path: "${params.results_publish_dir}",
@@ -182,33 +234,43 @@ workflow run_wf {
]
]
)
| setState([
"star_output_dir",
"nrReadsNrGenesPerChrom_dir",
"star_qc_metrics_dir",
"eset_dir",
"f_data_dir",
"p_data_dir",
]
)
fastq_publish_ch = grouped_ch
fastq_publish_ch = htrnaseq_ch
// The output from the htrnaseq workflow is on sample (i.e. pool) level
// Multiple sequencing runs may have contributes to the FASTQ files from this pool.
// So the fastq_output is a list of directories, one for each run.
// We assume that the names of the folders containing the FASTQ files are equal to the pool names.
| flatMap {id, state ->
def new_states = state.fastq_output.collect{fastq_dir ->
def run_id = fastq_dir.name // The folder name corresponds to the run
def sample = fastq_dir.parent.name // The parent folder name should be the sample
def new_id = "${run_id}/${sample}"
def fastq_files = fastq_dir.listFiles()
state.fastq_output.collect{fastq_dir ->
def run_id = fastq_dir.name
def new_id = "${run_id}/${state.sample_id}"
def new_state = [
"fastq_output": fastq_files,
"sample_id": sample,
"run_id": run_id
"fastq_output": fastq_dir.listFiles(),
"sample_id": state.sample_id,
"run_id": run_id,
"output": "${run_id}/${date}_htrnaseq_${version}/${state.sample_id}".toString()
]
return [new_id, new_state]
[new_id, new_state]
}
return new_states
}
// A folder containing the FASTQ files from a certain pool may be present in the state from
// multiple samples; if that pool contributed to the data from those samples.
// Those FASTQ files will only be published once by filtering out the duplicate events here.
| unique{it[0]}
| publish_fastqs.run(
fromState: { id, state ->
def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}")
[
input: state.fastq_output,
output: output_dir.toString(),
]
},
fromState: [
"input": "fastq_output",
"output": "output",
],
toState: { id, result, state -> state },
directives: [
publishDir: [
@@ -220,8 +282,8 @@ workflow run_wf {
)
emit:
grouped_ch
| map{ id, state -> [ id, [ _meta: [ join_id: state.run_id ] ] ] }
results_publish_ch
}
def get_version(inputFile) {
@@ -231,36 +293,3 @@ def get_version(inputFile) {
println("HT-RNAseq version to be used: ${version}")
return version
}
/*
* This function uses a heuristic to group a list of paths so that the level of nesting
* of IDs is represented in the output.
*
* We iterative of the path sections (subfolders) from the last (file) the first (root node).
* The first path segment that is common across all 'events' is the cutoff. We cutoff the paths
* at this level, select the unique elements from the list and use that as input for the next step.
*
* An optional offset allows one to shift the cutoff left or right.
*/
def reduce_paths(paths, offset = 0) {
def path_length = paths.collect{ it.getNameCount() }[0]
def unique_list = (path_length-1..0).collectEntries { i ->
[ (i): paths.collect{ it.getName(i) }.unique().size() ]
}
def cutoff = unique_list.find{ it.value == 1 }.key
def grouped_paths = paths.collect{ f -> "/" + f.subpath(0, cutoff+1+offset) }.unique()
println("")
println("Detecting the common path section to pass to the next step:")
print(" From: ")
print paths
println("")
print(" To: ")
print grouped_paths
println("")
return grouped_paths
}

18
src/workflows/runner/test.nf
View File

@@ -36,7 +36,8 @@ if (!params.containsKey("publish_dir")) {
params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString()
params.results_publish_dir = (file(params.publish_dir) / "results").toUriString()
assert file(params.fastq_publish_dir).isEmpty()
assert file(params.results_publish_dir).isEmpty()
// The module inherits the parameters defined before the include statement,
// therefore any parameters set afterwards will not be used by the module.
@@ -99,6 +100,17 @@ workflow test_wf {
| toSortedList()
| map {events ->
assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
events
}
| map {states ->
def output_state = states[0][1]
assert output_state.eset_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.rds", "VH02001614.rds"].toSet()
assert output_state.star_output_dir.listFiles().collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
["VH02001612", "VH02001614"].each{it ->
assert output_state.star_output_dir.resolve(it).listFiles().collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
}
assert output_state.star_qc_metrics_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
assert output_state.nrReadsNrGenesPerChrom_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
}
@@ -172,7 +184,7 @@ workflow test_wf {
assert files("${star_output}/VH02001614/*", 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("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
assert file("${expected_result_dir}/fData/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
} catch (Exception e) {
throw new WorkflowScriptErrorException("Integration test failed!", e)
@@ -309,7 +321,7 @@ workflow test_wf_with_lanes {
assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
assert file("${expected_result_dir}/report.html").isFile()
assert file("${expected_result_dir}/params.yaml").isFile()
assert file("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").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)

5
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,8 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -238,7 +237,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/eset/create_eset/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,8 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -215,7 +214,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/eset/create_fdata/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,8 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -229,7 +228,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/eset/create_pdata/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -187,7 +186,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -196,7 +195,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,8 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -171,7 +170,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/io/publish_fastqs/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

88
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -77,13 +77,90 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output arguments"
- name: "Output directory"
description: "Determines the name of output directories\n"
arguments:
- type: "file"
name: "--output"
name: "--star_output_dir"
info: null
default:
- "$id"
- "star_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--nrReadsNrGenesPerChrom_dir"
info: null
default:
- "nrReadsNrGenesPerChrom"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--star_qc_metrics_dir"
info: null
default:
- "starLogs"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--eset_dir"
info: null
default:
- "esets"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--f_data_dir"
info: null
default:
- "fData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--p_data_dir"
info: null
default:
- "pData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Output file arguments"
description: "Determines the name of output files"
arguments:
- type: "file"
name: "--run_params_output"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--html_report_output"
info: null
must_exist: true
create_parent: true
required: false
@@ -202,9 +279,8 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -234,7 +310,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/io/publish_results/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

374
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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -600,10 +600,41 @@ function ViashHelp {
echo " --run_params"
echo " type: file, required parameter, file must exist"
echo ""
echo "Output arguments:"
echo " --output"
echo "Output directory:"
echo " Determines the name of output directories"
echo ""
echo " --star_output_dir"
echo " type: file, output, file must exist"
echo " default: star_output"
echo ""
echo " --nrReadsNrGenesPerChrom_dir"
echo " type: file, output, file must exist"
echo " default: nrReadsNrGenesPerChrom"
echo ""
echo " --star_qc_metrics_dir"
echo " type: file, output, file must exist"
echo " default: starLogs"
echo ""
echo " --eset_dir"
echo " type: file, output, file must exist"
echo " default: esets"
echo ""
echo " --f_data_dir"
echo " type: file, output, file must exist"
echo " default: fData"
echo ""
echo " --p_data_dir"
echo " type: file, output, file must exist"
echo " default: pData"
echo ""
echo "Output file arguments:"
echo " Determines the name of output files"
echo ""
echo " --run_params_output"
echo " type: file, output, file must exist"
echo ""
echo " --html_report_output"
echo " type: file, output, file must exist"
echo " default: \$id"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
@@ -779,15 +810,92 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_RUN_PARAMS=$(ViashRemoveFlags "$1")
shift 1
;;
--output)
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
--star_output_dir)
[ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_OUTPUT_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_output_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--output=*)
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
--star_output_dir=*)
[ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir=*\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_OUTPUT_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--nrReadsNrGenesPerChrom_dir)
[ -n "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && ViashError Bad arguments for option \'--nrReadsNrGenesPerChrom_dir\': \'$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NRREADSNRGENESPERCHROM_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --nrReadsNrGenesPerChrom_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--nrReadsNrGenesPerChrom_dir=*)
[ -n "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && ViashError Bad arguments for option \'--nrReadsNrGenesPerChrom_dir=*\': \'$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--star_qc_metrics_dir)
[ -n "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && ViashError Bad arguments for option \'--star_qc_metrics_dir\': \'$VIASH_PAR_STAR_QC_METRICS_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_QC_METRICS_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_qc_metrics_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--star_qc_metrics_dir=*)
[ -n "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && ViashError Bad arguments for option \'--star_qc_metrics_dir=*\': \'$VIASH_PAR_STAR_QC_METRICS_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--eset_dir)
[ -n "$VIASH_PAR_ESET_DIR" ] && ViashError Bad arguments for option \'--eset_dir\': \'$VIASH_PAR_ESET_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ESET_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --eset_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--eset_dir=*)
[ -n "$VIASH_PAR_ESET_DIR" ] && ViashError Bad arguments for option \'--eset_dir=*\': \'$VIASH_PAR_ESET_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ESET_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--f_data_dir)
[ -n "$VIASH_PAR_F_DATA_DIR" ] && ViashError Bad arguments for option \'--f_data_dir\': \'$VIASH_PAR_F_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_F_DATA_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --f_data_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--f_data_dir=*)
[ -n "$VIASH_PAR_F_DATA_DIR" ] && ViashError Bad arguments for option \'--f_data_dir=*\': \'$VIASH_PAR_F_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_F_DATA_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--p_data_dir)
[ -n "$VIASH_PAR_P_DATA_DIR" ] && ViashError Bad arguments for option \'--p_data_dir\': \'$VIASH_PAR_P_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_P_DATA_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --p_data_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--p_data_dir=*)
[ -n "$VIASH_PAR_P_DATA_DIR" ] && ViashError Bad arguments for option \'--p_data_dir=*\': \'$VIASH_PAR_P_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_P_DATA_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--run_params_output)
[ -n "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && ViashError Bad arguments for option \'--run_params_output\': \'$VIASH_PAR_RUN_PARAMS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RUN_PARAMS_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --run_params_output. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--run_params_output=*)
[ -n "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && ViashError Bad arguments for option \'--run_params_output=*\': \'$VIASH_PAR_RUN_PARAMS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashRemoveFlags "$1")
shift 1
;;
--html_report_output)
[ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_HTML_REPORT_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --html_report_output. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--html_report_output=*)
[ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output=*\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
@@ -1020,8 +1128,23 @@ if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
fi
# filling in defaults
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
VIASH_PAR_OUTPUT="\$id"
if [ -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then
VIASH_PAR_STAR_OUTPUT_DIR="star_output"
fi
if [ -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then
VIASH_PAR_NRREADSNRGENESPERCHROM_DIR="nrReadsNrGenesPerChrom"
fi
if [ -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then
VIASH_PAR_STAR_QC_METRICS_DIR="starLogs"
fi
if [ -z ${VIASH_PAR_ESET_DIR+x} ]; then
VIASH_PAR_ESET_DIR="esets"
fi
if [ -z ${VIASH_PAR_F_DATA_DIR+x} ]; then
VIASH_PAR_F_DATA_DIR="fData"
fi
if [ -z ${VIASH_PAR_P_DATA_DIR+x} ]; then
VIASH_PAR_P_DATA_DIR="pData"
fi
# check whether required files exist
@@ -1181,8 +1304,29 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
fi
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_STAR_OUTPUT_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_STAR_OUTPUT_DIR")"
fi
if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")"
fi
if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_STAR_QC_METRICS_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_STAR_QC_METRICS_DIR")"
fi
if [ ! -z "$VIASH_PAR_ESET_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_ESET_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_ESET_DIR")"
fi
if [ ! -z "$VIASH_PAR_F_DATA_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_F_DATA_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_F_DATA_DIR")"
fi
if [ ! -z "$VIASH_PAR_P_DATA_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_P_DATA_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_P_DATA_DIR")"
fi
if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
@@ -1271,10 +1415,45 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS")" )
VIASH_PAR_RUN_PARAMS=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_OUTPUT_DIR")" )
VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_OUTPUT_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_STAR_OUTPUT_DIR" )
fi
if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")" )
VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" )
fi
if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_QC_METRICS_DIR")" )
VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_QC_METRICS_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_STAR_QC_METRICS_DIR" )
fi
if [ ! -z "$VIASH_PAR_ESET_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ESET_DIR")" )
VIASH_PAR_ESET_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_ESET_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_ESET_DIR" )
fi
if [ ! -z "$VIASH_PAR_F_DATA_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_F_DATA_DIR")" )
VIASH_PAR_F_DATA_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_F_DATA_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_F_DATA_DIR" )
fi
if [ ! -z "$VIASH_PAR_P_DATA_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_P_DATA_DIR")" )
VIASH_PAR_P_DATA_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_P_DATA_DIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_P_DATA_DIR" )
fi
if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS_OUTPUT")" )
VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_PARAMS_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_HTML_REPORT_OUTPUT")" )
VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_HTML_REPORT_OUTPUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_HTML_REPORT_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
@@ -1353,7 +1532,14 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
$( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
$( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; 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 ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
$( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
$( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
$( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_eset_dir='&'#" ; else echo "# par_eset_dir="; fi )
$( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
$( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; 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 )
@@ -1376,48 +1562,97 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
## VIASH END
#!/bin/bash
echo "Publishing \$par_input -> \$par_output"
set -eo pipefail
echo "Publishing results to multiple output directories"
# Create output directories for multiple files
echo "Creating output directories..."
path_pars=(
par_star_output_dir
par_nrReadsNrGenesPerChrom_dir
par_star_qc_metrics_dir
par_eset_dir
par_f_data_dir
par_p_data_dir
par_html_report_output
par_run_params_output
)
for par in \${path_pars[@]}; do
curr_val="\${!par}"
new_value=\$(realpath --canonicalize-missing "\$curr_val")
declare -g "\$par=\$new_value"
done
mkdir -p "\$par_star_output_dir" && echo "\$par_star_output_dir created"
mkdir -p "\$par_nrReadsNrGenesPerChrom_dir" && echo "\$par_nrReadsNrGenesPerChrom_dir created"
mkdir -p "\$par_star_qc_metrics_dir" && echo "\$par_star_qc_metrics_dir created"
mkdir -p "\$par_eset_dir" && echo "\$par_eset_dir created"
mkdir -p "\$par_f_data_dir" && echo "\$par_f_data_dir created"
mkdir -p "\$par_p_data_dir" && echo "\$par_p_data_dir created"
echo
echo "Creating directory if it does not exist:"
mkdir -p "\$par_output" && echo "\$par_output created"
echo
echo "Copying files..."
echo "Copying STAR output files..."
IFS=";" read -ra star_output <<<\$par_star_output
IFS=";" read -ra nrReadsNrGenesPerChrom <<<\$par_nrReadsNrGenesPerChrom
IFS=";" read -ra star_qc_metrics <<<\$par_star_qc_metrics
IFS=";" read -ra eset <<<\$par_eset
IFS=";" read -ra f_data <<<\$par_f_data
IFS=";" read -ra p_data <<<\$par_p_data
for i in "\${star_output[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_star_output_dir/"
cp -rL "\$i" "\$par_star_output_dir/"
done
echo
echo "Copying nrReadsNrGenesPerChrom files..."
IFS=";" read -ra nrReadsNrGenesPerChrom <<<\$par_nrReadsNrGenesPerChrom
for i in "\${nrReadsNrGenesPerChrom[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_nrReadsNrGenesPerChrom_dir/"
cp -rL "\$i" "\$par_nrReadsNrGenesPerChrom_dir/"
done
echo
echo "Copying STAR QC metrics files..."
IFS=";" read -ra star_qc_metrics <<<\$par_star_qc_metrics
for i in "\${star_qc_metrics[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_star_qc_metrics_dir/"
cp -rL "\$i" "\$par_star_qc_metrics_dir/"
done
echo
echo "Copying eset files..."
IFS=";" read -ra eset <<<\$par_eset
for i in "\${eset[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_eset_dir/"
cp -rL "\$i" "\$par_eset_dir/"
done
echo
echo "Copying f_data files..."
IFS=";" read -ra f_data <<<\$par_f_data
for i in "\${f_data[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_f_data_dir/"
cp -rL "\$i" "\$par_f_data_dir/"
done
echo
echo "Copying p_data files..."
IFS=";" read -ra p_data <<<\$par_p_data
for i in "\${p_data[@]}"; do
cp -rL "\$i" "\$par_output/"
echo "Copying \$i to \$par_p_data_dir/"
cp -rL "\$i" "\$par_p_data_dir/"
done
cp -rL "\$par_html_report" "\$par_output/"
echo
echo "Copying single files directly..."
mkdir -p \$(dirname "\$par_html_report_output")
echo "Copying \$par_html_report to \$par_html_report_output"
cp -L "\$par_html_report" "\$par_html_report_output"
cp -rL "\$par_run_params" "\$par_output/"
echo "Copying \$par_run_params to \$par_run_params_output"
mkdir -p \$(dirname "\$par_run_params_output")
cp -L "\$par_run_params" "\$par_run_params_output"
echo
echo "Publishing completed successfully!"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
@@ -1512,8 +1747,29 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then
VIASH_PAR_RUN_PARAMS=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_OUTPUT_DIR")
fi
if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
VIASH_PAR_NRREADSNRGENESPERCHROM_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR")
fi
if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
VIASH_PAR_STAR_QC_METRICS_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_QC_METRICS_DIR")
fi
if [ ! -z "$VIASH_PAR_ESET_DIR" ]; then
VIASH_PAR_ESET_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_ESET_DIR")
fi
if [ ! -z "$VIASH_PAR_F_DATA_DIR" ]; then
VIASH_PAR_F_DATA_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_F_DATA_DIR")
fi
if [ ! -z "$VIASH_PAR_P_DATA_DIR" ]; then
VIASH_PAR_P_DATA_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_P_DATA_DIR")
fi
if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS_OUTPUT")
fi
if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_HTML_REPORT_OUTPUT")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
@@ -1531,8 +1787,36 @@ fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then
ViashError "Output file '$VIASH_PAR_STAR_OUTPUT_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ] && [ ! -e "$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR" ]; then
ViashError "Output file '$VIASH_PAR_NRREADSNRGENESPERCHROM_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_STAR_QC_METRICS_DIR" ] && [ ! -e "$VIASH_PAR_STAR_QC_METRICS_DIR" ]; then
ViashError "Output file '$VIASH_PAR_STAR_QC_METRICS_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_ESET_DIR" ] && [ ! -e "$VIASH_PAR_ESET_DIR" ]; then
ViashError "Output file '$VIASH_PAR_ESET_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_F_DATA_DIR" ] && [ ! -e "$VIASH_PAR_F_DATA_DIR" ]; then
ViashError "Output file '$VIASH_PAR_F_DATA_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_P_DATA_DIR" ] && [ ! -e "$VIASH_PAR_P_DATA_DIR" ]; then
ViashError "Output file '$VIASH_PAR_P_DATA_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then
ViashError "Output file '$VIASH_PAR_RUN_PARAMS_OUTPUT' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -e "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then
ViashError "Output file '$VIASH_PAR_HTML_REPORT_OUTPUT' does not exist."
exit 1
fi

5
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,8 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -317,7 +316,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/parallel_map/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,8 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -247,7 +246,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/report/create_report/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -236,7 +235,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/stats/combine_star_logs/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -220,7 +219,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/stats/generate_pool_statistics/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -260,9 +260,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -292,7 +291,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/stats/generate_well_statistics/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -151,9 +151,8 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -183,7 +182,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/executable/utils/save_params/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

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="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.created="2025-09-02T07:26:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.revision="92755e84e7e2b17cc44664388d6fbb444a26cffd"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

5
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,8 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -238,7 +237,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/eset/create_eset/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/eset/create_eset/main.nf
View File

@@ -3309,9 +3309,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3330,7 +3329,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,8 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -215,7 +214,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/eset/create_fdata/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3279,9 +3279,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3300,7 +3299,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,8 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -229,7 +228,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/eset/create_pdata/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3293,9 +3293,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3314,7 +3313,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -187,7 +186,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3233,9 +3233,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3254,7 +3253,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -196,7 +195,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3244,9 +3244,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3265,7 +3264,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,8 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -171,7 +170,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/io/publish_fastqs/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/io/publish_fastqs/main.nf
View File

@@ -3207,9 +3207,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3228,7 +3227,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

88
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -77,13 +77,90 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output arguments"
- name: "Output directory"
description: "Determines the name of output directories\n"
arguments:
- type: "file"
name: "--output"
name: "--star_output_dir"
info: null
default:
- "$id"
- "star_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--nrReadsNrGenesPerChrom_dir"
info: null
default:
- "nrReadsNrGenesPerChrom"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--star_qc_metrics_dir"
info: null
default:
- "starLogs"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--eset_dir"
info: null
default:
- "esets"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--f_data_dir"
info: null
default:
- "fData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--p_data_dir"
info: null
default:
- "pData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Output file arguments"
description: "Determines the name of output files"
arguments:
- type: "file"
name: "--run_params_output"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--html_report_output"
info: null
must_exist: true
create_parent: true
required: false
@@ -202,9 +279,8 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -234,7 +310,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/io/publish_results/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

203
target/nextflow/io/publish_results/main.nf
View File

@@ -3121,13 +3121,14 @@ meta = [
]
},
{
"name" : "Output arguments",
"name" : "Output directory",
"description" : "Determines the name of output directories\n",
"arguments" : [
{
"type" : "file",
"name" : "--output",
"name" : "--star_output_dir",
"default" : [
"$id"
"star_output"
],
"must_exist" : true,
"create_parent" : true,
@@ -3135,6 +3136,97 @@ meta = [
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--nrReadsNrGenesPerChrom_dir",
"default" : [
"nrReadsNrGenesPerChrom"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--star_qc_metrics_dir",
"default" : [
"starLogs"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--eset_dir",
"default" : [
"esets"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--f_data_dir",
"default" : [
"fData"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--p_data_dir",
"default" : [
"pData"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
}
]
},
{
"name" : "Output file arguments",
"description" : "Determines the name of output files",
"arguments" : [
{
"type" : "file",
"name" : "--run_params_output",
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--html_report_output",
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
}
]
}
@@ -3277,9 +3369,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3298,7 +3389,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"
@@ -3342,7 +3433,14 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#'
$( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi )
$( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; 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 ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi )
$( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi )
$( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi )
$( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_eset_dir='&'#" ; else echo "# par_eset_dir="; fi )
$( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi )
$( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; 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 )
@@ -3365,48 +3463,97 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
## VIASH END
#!/bin/bash
echo "Publishing \\$par_input -> \\$par_output"
set -eo pipefail
echo "Publishing results to multiple output directories"
# Create output directories for multiple files
echo "Creating output directories..."
path_pars=(
par_star_output_dir
par_nrReadsNrGenesPerChrom_dir
par_star_qc_metrics_dir
par_eset_dir
par_f_data_dir
par_p_data_dir
par_html_report_output
par_run_params_output
)
for par in \\${path_pars[@]}; do
curr_val="\\${!par}"
new_value=\\$(realpath --canonicalize-missing "\\$curr_val")
declare -g "\\$par=\\$new_value"
done
mkdir -p "\\$par_star_output_dir" && echo "\\$par_star_output_dir created"
mkdir -p "\\$par_nrReadsNrGenesPerChrom_dir" && echo "\\$par_nrReadsNrGenesPerChrom_dir created"
mkdir -p "\\$par_star_qc_metrics_dir" && echo "\\$par_star_qc_metrics_dir created"
mkdir -p "\\$par_eset_dir" && echo "\\$par_eset_dir created"
mkdir -p "\\$par_f_data_dir" && echo "\\$par_f_data_dir created"
mkdir -p "\\$par_p_data_dir" && echo "\\$par_p_data_dir created"
echo
echo "Creating directory if it does not exist:"
mkdir -p "\\$par_output" && echo "\\$par_output created"
echo
echo "Copying files..."
echo "Copying STAR output files..."
IFS=";" read -ra star_output <<<\\$par_star_output
IFS=";" read -ra nrReadsNrGenesPerChrom <<<\\$par_nrReadsNrGenesPerChrom
IFS=";" read -ra star_qc_metrics <<<\\$par_star_qc_metrics
IFS=";" read -ra eset <<<\\$par_eset
IFS=";" read -ra f_data <<<\\$par_f_data
IFS=";" read -ra p_data <<<\\$par_p_data
for i in "\\${star_output[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_star_output_dir/"
cp -rL "\\$i" "\\$par_star_output_dir/"
done
echo
echo "Copying nrReadsNrGenesPerChrom files..."
IFS=";" read -ra nrReadsNrGenesPerChrom <<<\\$par_nrReadsNrGenesPerChrom
for i in "\\${nrReadsNrGenesPerChrom[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_nrReadsNrGenesPerChrom_dir/"
cp -rL "\\$i" "\\$par_nrReadsNrGenesPerChrom_dir/"
done
echo
echo "Copying STAR QC metrics files..."
IFS=";" read -ra star_qc_metrics <<<\\$par_star_qc_metrics
for i in "\\${star_qc_metrics[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_star_qc_metrics_dir/"
cp -rL "\\$i" "\\$par_star_qc_metrics_dir/"
done
echo
echo "Copying eset files..."
IFS=";" read -ra eset <<<\\$par_eset
for i in "\\${eset[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_eset_dir/"
cp -rL "\\$i" "\\$par_eset_dir/"
done
echo
echo "Copying f_data files..."
IFS=";" read -ra f_data <<<\\$par_f_data
for i in "\\${f_data[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_f_data_dir/"
cp -rL "\\$i" "\\$par_f_data_dir/"
done
echo
echo "Copying p_data files..."
IFS=";" read -ra p_data <<<\\$par_p_data
for i in "\\${p_data[@]}"; do
cp -rL "\\$i" "\\$par_output/"
echo "Copying \\$i to \\$par_p_data_dir/"
cp -rL "\\$i" "\\$par_p_data_dir/"
done
cp -rL "\\$par_html_report" "\\$par_output/"
echo
echo "Copying single files directly..."
mkdir -p \\$(dirname "\\$par_html_report_output")
echo "Copying \\$par_html_report to \\$par_html_report_output"
cp -L "\\$par_html_report" "\\$par_html_report_output"
cp -rL "\\$par_run_params" "\\$par_output/"
echo "Copying \\$par_run_params to \\$par_run_params_output"
mkdir -p \\$(dirname "\\$par_run_params_output")
cp -L "\\$par_run_params" "\\$par_run_params_output"
echo
echo "Publishing completed successfully!"
VIASHMAIN
bash "$tempscript"
'''

73
target/nextflow/io/publish_results/nextflow_schema.json
View File

@@ -85,17 +85,73 @@
}
}
},
"output arguments": {
"title": "Output arguments",
"output directory": {
"title": "Output directory",
"type": "object",
"description": "No description",
"description": "Determines the name of output directories\n",
"properties": {
"output": {
"star_output_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id\"`, direction: `output`. ",
"default": "$id"
"help_text": "Type: `file`, multiple: `False`, default: `\"star_output\"`, direction: `output`. ",
"default": "star_output"
},
"nrReadsNrGenesPerChrom_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"nrReadsNrGenesPerChrom\"`, direction: `output`. ",
"default": "nrReadsNrGenesPerChrom"
},
"star_qc_metrics_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"starLogs\"`, direction: `output`. ",
"default": "starLogs"
},
"eset_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"esets\"`, direction: `output`. ",
"default": "esets"
},
"f_data_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"fData\"`, direction: `output`. ",
"default": "fData"
},
"p_data_dir": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"pData\"`, direction: `output`. ",
"default": "pData"
}
}
},
"output file arguments": {
"title": "Output file arguments",
"type": "object",
"description": "Determines the name of output files",
"properties": {
"run_params_output": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_params_output\"`, direction: `output`. ",
"default": "$id.$key.run_params_output"
},
"html_report_output": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.html_report_output\"`, direction: `output`. ",
"default": "$id.$key.html_report_output"
}
}
},
@@ -117,7 +173,10 @@
"$ref": "#/$defs/input arguments"
},
{
"$ref": "#/$defs/output arguments"
"$ref": "#/$defs/output directory"
},
{
"$ref": "#/$defs/output file arguments"
},
{
"$ref": "#/$defs/nextflow input-output arguments"

5
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,8 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -317,7 +316,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/parallel_map/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/parallel_map/main.nf
View File

@@ -3379,9 +3379,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3400,7 +3399,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,8 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -247,7 +246,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/report/create_report/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/report/create_report/main.nf
View File

@@ -3323,9 +3323,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3344,7 +3343,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -236,7 +235,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/stats/combine_star_logs/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3295,9 +3295,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3316,7 +3315,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -220,7 +219,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/stats/generate_pool_statistics/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3279,9 +3279,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3300,7 +3299,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -260,9 +260,8 @@ 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: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -292,7 +291,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/stats/generate_well_statistics/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3361,9 +3361,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3382,7 +3381,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -160,9 +160,8 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
package_config:
@@ -194,7 +193,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/utils/concatRuns/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3229,9 +3229,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3250,7 +3249,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -169,9 +169,8 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -201,7 +200,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/utils/listInputDir/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3236,9 +3236,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3257,7 +3256,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/utils/save_params/.config.vsh.yaml
View File

@@ -151,9 +151,8 @@ build_info:
output: "target/nextflow/utils/save_params"
executable: "target/nextflow/utils/save_params/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -183,7 +182,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/utils/save_params/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

7
target/nextflow/utils/save_params/main.nf
View File

@@ -3223,9 +3223,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/utils/save_params",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3244,7 +3243,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

5
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -345,9 +345,8 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
dependencies:
- "target/nextflow/stats/combine_star_logs"
- "target/nextflow/stats/generate_pool_statistics"
@@ -390,7 +389,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

2
target/nextflow/workflows/htrnaseq/_viash.yaml
View File

@@ -14,7 +14,7 @@ info:
dest: resources_test
config_mods: |
.requirements.commands := ['ps']
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
.runners[.type == 'nextflow'].config.script += 'includeConfig("nextflow_labels.config")'
.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main

8
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3484,9 +3484,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-14-gd70fdf2"
"git_commit" : "92755e84e7e2b17cc44664388d6fbb444a26cffd",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3505,7 +3504,7 @@ meta = [
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"
@@ -3893,7 +3892,6 @@ workflow run_wf {
| setState([
"star_output": "star_output",
"fastq_output": "fastq_output_directory",
"star_output": "star_output",
"nrReadsNrGenesPerChrom": "nrReadsNrGenesPerChromPool",
"star_qc_metrics": "star_qc_metrics",
"eset": "eset",

76
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -121,11 +121,81 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "file"
name: "--star_output_dir"
info: null
default:
- "star_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--nrReadsNrGenesPerChrom_dir"
info: null
default:
- "nrReadsNrGenesPerChrom"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--star_qc_metrics_dir"
info: null
default:
- "starLogs"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--eset_dir"
info: null
default:
- "esets"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--f_data_dir"
info: null
default:
- "fData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--p_data_dir"
info: null
default:
- "pData"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
is_executable: true
entrypoint: "run_wf"
- type: "file"
path: "disable_publishfiles_process.config"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
@@ -226,6 +296,7 @@ runners:
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"disable_publishfiles_process.config\")"
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
@@ -241,9 +312,8 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_commit: "92755e84e7e2b17cc44664388d6fbb444a26cffd"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-14-gd70fdf2"
dependencies:
- "target/nextflow/utils/listInputDir"
- "target/nextflow/workflows/htrnaseq"
@@ -279,7 +349,7 @@ package_config:
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ += 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"

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