vsh/htrnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch non_alphanumerical_sample_names with version non_alphanumerical_sample_names (61bdd2e)

Browse Source 
Build pipeline: viash-hub.htrnaseq.non-alphanumerical-sample-names-bpjrz

Source commit: 61bdd2eff7

Source message: Update CHANGELOG
This commit is contained in:
CI
2025-08-01 10:33:05 +00:00
parent 077772a26d
commit f9a30ab928
70 changed files with 357 additions and 183 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
CHANGELOG.md
View File

@@ -1,3 +1,11 @@
# htrnaseq v0.9.1
## Bug fixes
* Reverted functionality to set `fastq_publish_dir` and `results_publish_dir` using fromState (PR #64).
* `runner`: fix detection of FASTQ files with non-numerical characters in the sample name (PR #65).
# htrnaseq v0.9.0
## Breaking changes

5
src/workflows/runner/config.vsh.yaml
View File

@@ -60,6 +60,11 @@ resources:
path: main.nf
entrypoint: run_wf
test_resources:
- type: nextflow_script
path: test.nf
entrypoint: test_wf
dependencies:
- name: utils/listInputDir
repository: local

13
src/workflows/runner/integration_test.sh Executable file
View File

@@ -0,0 +1,13 @@
# get the root of the directory
REPO_ROOT=$(git rev-parse --show-toplevel)
# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"
nextflow \
run . \
-main-script src/workflows/runner/test.nf \
-config ./src/config/labels.config \
-entry test_wf \
-resume \
-profile docker,local

31
src/workflows/runner/main.nf
View File

@@ -16,24 +16,6 @@ workflow run_wf {
return [id, new_state]
}
// When this workflow is being used as a subworkflow, the publish directories might be defined
// in the state and not in params. The following snippets make sure the values are copied from state to params.
set_publish_dirs_channel = raw_ch
| toSortedList()
| map {ids_and_states ->
def publish_dir_arguments = ["results_publish_dir", "fastq_publish_dir"]
for (publish_dir_arg in publish_dir_arguments) {
if (!params.containsKey(publish_dir_arg)) {
def state_items = ids_and_states.collect{it[1].get(publish_dir_arg)}
assert state_items.toSet().size() == state_items.size(), "Items for '${publish_dir_arg}' must be unique! Found ${state_items}"
params[publish_dir_arg] = state_items[0]
}
}
ids_and_states
}
save_params_ch = input_ch
| toSortedList()
| map { states ->
@@ -172,11 +154,7 @@ workflow run_wf {
}
// Use combine here in order to be sure tha the publish dirs are set in params
// set_publish_dirs_channel should contain 1 event; so the result of the combine
// contains the events from grouped_with_params_list_ch
results_publish_ch = grouped_with_params_list_ch.combine(set_publish_dirs_channel)
| map {event -> [event[0], event[1]]}
results_publish_ch = grouped_with_params_list_ch
| publish_results.run(
fromState: { id, state ->
def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
@@ -204,7 +182,7 @@ workflow run_wf {
]
)
fastq_publish_split_ch = grouped_ch
fastq_publish_ch = grouped_ch
| flatMap{id, state ->
def new_states = state.fastq_output.collect{fastq_dir ->
def run_id = fastq_dir.name // The folder name corresponds to the run
@@ -220,9 +198,6 @@ workflow run_wf {
}
return new_states
}
fastq_publish_ch = fastq_publish_split_ch.combine(set_publish_dirs_channel)
| map{event -> [event[0], event[1]]}
| publish_fastqs.run(
fromState: { id, state ->
def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
@@ -287,4 +262,4 @@ def reduce_paths(paths, offset = 0) {
println("")
return grouped_paths
}
}

4
src/workflows/runner/nextflow.config
View File

@@ -2,6 +2,10 @@ manifest {
nextflowVersion = '!>=20.12.1-edge'
}
params {
rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString()
}
process {
withName: publishStatesProc {
publishDir = [ enabled: false ]

181
src/workflows/runner/test.nf
View File

@@ -0,0 +1,181 @@
import java.nio.file.Files
import nextflow.exception.WorkflowScriptErrorException
def viash_config = java.nio.file.Paths.get("${params.rootDir}/target/nextflow/workflows/runner/_viash.yaml")
def get_version(inputFile) {
def yamlSlurper = new groovy.yaml.YamlSlurper()
def loaded_viash_config = yamlSlurper.parse(file(inputFile))
def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
println("HT-RNAseq version to be used: ${version}")
return version
}
// Create temporary directory for the publish_dir if it is not defined
if (!params.containsKey("publish_dir") && params.containsKey("publishDir")) {
params.publish_dir = params.publishDir
}
if (!params.containsKey("publish_dir")) {
def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test")
println "Created temp directory: $tempDir"
// Register shutdown hook to delete it on JVM exit
Runtime.runtime.addShutdownHook(new Thread({
try {
// Delete directory recursively
Files.walk(tempDir)
.sorted(Comparator.reverseOrder())
.forEach { Files.delete(it) }
println "Deleted temp directory: $tempDir"
} catch (Exception e) {
println "Failed to delete temp directory: $e"
}
}))
params.publish_dir = tempDir
}
params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString()
params.results_publish_dir = (file(params.publish_dir) / "results").toUriString()
// The module inherits the parameters defined before the include statement,
// therefore any parameters set afterwards will not be used by the module.
include { runner } from params.rootDir + "/target/nextflow/workflows/runner/main.nf"
params.resources_test = params.rootDir + "/resources_test"
workflow test_wf {
pipeline_version = get_version(viash_config)
resources_test = file(params.resources_test)
// results_publish_dir and results_publish_dir are inherited using params
// but they must be defined in the state as well because viash will check
// if all arguments are present in the hashmap
output_ch = Channel.fromList([
[
id: "run_1",
input: resources_test.resolve("10k/SRR14730301"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
],
[
id: "run_2",
input: resources_test.resolve("10k/SRR14730301"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
],
[
id: "run_3",
input:resources_test.resolve("10k/SRR14730302"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
]
])
| map { state -> [state.id, state]}
| runner.run(
toState: { id, output, state -> output + [orig_input: state.input] }
)
| view { output ->
assert output.size() == 2 : "outputs should contain two elements; [id, file]"
"Output: $output"
}
tosortedlistch = output_ch
| toSortedList()
| map {events ->
assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
}
workflow.onComplete = {
try {
// Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
// So in order for the assert statement to work (or allow other errors to let the tests to fail)
// We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
// The error message will show up in .nextflow.log
def fastq_subdir = file("${params.fastq_publish_dir}")
assert fastq_subdir.isDirectory()
def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
def expected_run_folders = ["run_1", "run_2", "run_3"].toSet()
assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
unique_dirs = [
"run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
"run2": files("${fastq_subdir.toUriString()}/run_2/*_htrnaseq_${pipeline_version}", type: 'any'),
"run3": files("${fastq_subdir.toUriString()}/run_3/*_htrnaseq_${pipeline_version}", type: 'any'),
]
assert unique_dirs.every{it.value.size() == 1}
unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
assert unique_dirs.every{it.value.isDirectory()}
assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
def expected_samples = [
"run1": "VH02001612",
"run2": "VH02001612",
"run3": "VH02001614"
]
unique_dirs.each{_key, _value ->
def expected_sample = expected_samples[_key]
def expected_sample_dir = _value.resolve(expected_sample)
assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
def expected_fastq_files = [
"A1_R1_001.fastq", "A1_R2_001.fastq",
"B1_R1_001.fastq", "B1_R2_001.fastq",
"unknown_R1_001.fastq", "unknown_R2_001.fastq"]
def found_files = files("${expected_sample_dir}/*.fastq", type: 'any')
assert found_files.every{it.isFile()}
assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
}
def results_subdir = file("${params.results_publish_dir}")
assert fastq_subdir.isDirectory()
def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
assert expected_subdir.isDirectory()
def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
assert expected_result_dir.size() == 1
expected_result_dir = expected_result_dir[0]
assert expected_result_dir.isDirectory()
def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
assert found_esets.size() == 2
assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
assert found_pdata.size() == 2
assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
assert found_nr_genes_nr_reads.size() == 2
assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
assert found_star_logs.size() == 2
assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
def star_output = file("${expected_result_dir}/star_output", type: 'any')
assert star_output.isDirectory()
assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
assert files("${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()
} catch (Exception e) {
throw new WorkflowScriptErrorException("Integration test failed!", e)
}
}
}

4
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,9 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:06Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,9 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:06Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,9 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:05Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:42Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:06Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:08Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -202,9 +202,9 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
LABEL org.opencontainers.image.created="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,9 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,9 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:06Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -270,9 +270,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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

@@ -461,9 +461,9 @@ 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="2025-08-01T08:07:05Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:42Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -151,9 +151,9 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

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="2025-08-01T08:07:07Z"
LABEL org.opencontainers.image.created="2025-08-01T09:41:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4c165f546fe37dd8bbead7d593bd26209247d2f2"
LABEL org.opencontainers.image.revision="61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
LABEL org.opencontainers.image.version="non_alphanumerical_sample_names"
VIASHDOCKER

4
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,9 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/eset/create_eset/main.nf
View File

@@ -3309,9 +3309,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,9 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3279,9 +3279,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,9 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3293,9 +3293,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3233,9 +3233,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3244,9 +3244,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/io/publish_fastqs/main.nf
View File

@@ -3207,9 +3207,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -202,9 +202,9 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/io/publish_results/main.nf
View File

@@ -3277,9 +3277,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,9 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/parallel_map/main.nf
View File

@@ -3379,9 +3379,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,9 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/report/create_report/main.nf
View File

@@ -3323,9 +3323,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3295,9 +3295,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3279,9 +3279,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -270,9 +270,9 @@ 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: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3374,9 +3374,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -160,9 +160,9 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
package_config:

4
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3229,9 +3229,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -171,9 +171,9 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3239,9 +3239,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/utils/save_params/.config.vsh.yaml
View File

@@ -151,9 +151,9 @@ build_info:
output: "target/nextflow/utils/save_params"
executable: "target/nextflow/utils/save_params/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/utils/save_params/main.nf
View File

@@ -3223,9 +3223,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/utils/save_params",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -345,9 +345,9 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
dependencies:
- "target/nextflow/stats/combine_star_logs"
- "target/nextflow/stats/generate_pool_statistics"

4
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3484,9 +3484,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

9
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -127,6 +127,11 @@ resources:
path: "_viash.yaml"
dest: "_viash.yaml"
description: "Runner for HT RNA-seq pipeline"
test_resources:
- type: "nextflow_script"
path: "test.nf"
is_executable: true
entrypoint: "test_wf"
info: null
status: "enabled"
scope:
@@ -230,9 +235,9 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
dependencies:
- "target/nextflow/utils/listInputDir"
- "target/nextflow/workflows/htrnaseq"

41
target/nextflow/workflows/runner/main.nf
View File

@@ -3191,6 +3191,14 @@ meta = [
}
],
"description" : "Runner for HT RNA-seq pipeline",
"test_resources" : [
{
"type" : "nextflow_script",
"path" : "test.nf",
"is_executable" : true,
"entrypoint" : "test_wf"
}
],
"status" : "enabled",
"scope" : {
"image" : "public",
@@ -3325,9 +3333,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3399,24 +3407,6 @@ workflow run_wf {
return [id, new_state]
}
// When this workflow is being used as a subworkflow, the publish directories might be defined
// in the state and not in params. The following snippets make sure the values are copied from state to params.
set_publish_dirs_channel = raw_ch
| toSortedList()
| map {ids_and_states ->
def publish_dir_arguments = ["results_publish_dir", "fastq_publish_dir"]
for (publish_dir_arg in publish_dir_arguments) {
if (!params.containsKey(publish_dir_arg)) {
def state_items = ids_and_states.collect{it[1].get(publish_dir_arg)}
assert state_items.toSet().size() == state_items.size(), "Items for '${publish_dir_arg}' must be unique! Found ${state_items}"
params[publish_dir_arg] = state_items[0]
}
}
ids_and_states
}
save_params_ch = input_ch
| toSortedList()
| map { states ->
@@ -3555,11 +3545,7 @@ workflow run_wf {
}
// Use combine here in order to be sure tha the publish dirs are set in params
// set_publish_dirs_channel should contain 1 event; so the result of the combine
// contains the events from grouped_with_params_list_ch
results_publish_ch = grouped_with_params_list_ch.combine(set_publish_dirs_channel)
| map {event -> [event[0], event[1]]}
results_publish_ch = grouped_with_params_list_ch
| publish_results.run(
fromState: { id, state ->
def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
@@ -3587,7 +3573,7 @@ workflow run_wf {
]
)
fastq_publish_split_ch = grouped_ch
fastq_publish_ch = grouped_ch
| flatMap{id, state ->
def new_states = state.fastq_output.collect{fastq_dir ->
def run_id = fastq_dir.name // The folder name corresponds to the run
@@ -3603,9 +3589,6 @@ workflow run_wf {
}
return new_states
}
fastq_publish_ch = fastq_publish_split_ch.combine(set_publish_dirs_channel)
| map{event -> [event[0], event[1]]}
| publish_fastqs.run(
fromState: { id, state ->
def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"

4
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -217,9 +217,9 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"

4
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3319,9 +3319,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/well_metadata/.config.vsh.yaml
View File

@@ -215,9 +215,9 @@ build_info:
output: "target/nextflow/workflows/well_metadata"
executable: "target/nextflow/workflows/well_metadata/main.nf"
viash_version: "0.9.4"
git_commit: "4c165f546fe37dd8bbead7d593bd26209247d2f2"
git_commit: "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-11-g4c165f5"
git_tag: "v0.7.2-14-g61bdd2e"
package_config:
name: "htrnaseq"
version: "non_alphanumerical_sample_names"

4
target/nextflow/workflows/well_metadata/main.nf
View File

@@ -3299,9 +3299,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_metadata",
"viash_version" : "0.9.4",
"git_commit" : "4c165f546fe37dd8bbead7d593bd26209247d2f2",
"git_commit" : "61bdd2eff7622d9d8626e9a3514b832d89dcf2f2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-11-g4c165f5"
"git_tag" : "v0.7.2-14-g61bdd2e"
},
"package_config" : {
"name" : "htrnaseq",