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Build branch main with version main (10d3b38)

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Build pipeline: viash-hub.htrnaseq.main-77sg6

Source commit: 10d3b382d6

Source message: Add runner integration tests, revert ec0dd8b (#64)
This commit is contained in:
CI
2025-08-01 10:14:18 +00:00
parent 060c9c49a8
commit 6f76b49468
71 changed files with 373 additions and 217 deletions
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52
target/nextflow/workflows/runner/main.nf
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@@ -3150,17 +3150,6 @@ meta = [
}
]
},
{
"name" : "Annotation flags",
"arguments" : [
{
"type" : "boolean_true",
"name" : "--plain_output",
"description" : "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
"direction" : "input"
}
]
},
{
"name" : "Publish arguments",
"arguments" : [
@@ -3202,6 +3191,14 @@ meta = [
}
],
"description" : "Runner for HT RNA-seq pipeline",
"test_resources" : [
{
"type" : "nextflow_script",
"path" : "test.nf",
"is_executable" : true,
"entrypoint" : "test_wf"
}
],
"status" : "enabled",
"scope" : {
"image" : "public",
@@ -3336,9 +3333,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.4",
"git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
"git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-9-g0e87de8"
"git_tag" : "v0.7.2-11-g10d3b38"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3551,20 +3548,10 @@ workflow run_wf {
results_publish_ch = grouped_with_params_list_ch
| publish_results.run(
fromState: { id, state ->
def project = (state.plain_output) ? id : "${state.project_id}"
def experiment = (state.plain_output) ? id : "${state.experiment_id}"
def id0 = "${project}/${experiment}"
def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}"
def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}"
if (id == id2) {
println("Publising results to ${params.results_publish_dir}")
} else {
println("Publising results to ${params.results_publish_dir}/${id2}")
}
def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
println("Publising results to ${params.results_publish_dir}/${output_dir}")
[
star_output: state.star_output,
star_output: state.star_output,
nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
star_qc_metrics: state.star_qc_metrics,
@@ -3573,7 +3560,7 @@ workflow run_wf {
p_data: state.p_data,
html_report: state.html_report,
run_params: state.run_params,
output: "${id2}"
output: output_dir.toString()
]
},
toState: { id, result, state -> state },
@@ -3604,19 +3591,12 @@ workflow run_wf {
}
| publish_fastqs.run(
fromState: { id, state ->
def id0 = state.run_id
def id1 = (state.plain_output) ? id : "${id0}/${date}"
def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}/${state.sample_id}"
if (id == id2) {
println("Publising fastqs to ${params.fastq_publish_dir}")
} else {
println("Publising fastqs to ${params.fastq_publish_dir}/${id2}")
}
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: "${id2}",
output: output_dir.toString(),
]
},
toState: { id, result, state -> state },