CI
50ab36217a
Build pipeline: viash-hub.demultiplex.main-wxzkf
Source commit: 6e71519815
Source message: Replace Falco with FastQC (#51)
109 lines
4.0 KiB
Plaintext
109 lines
4.0 KiB
Plaintext
def date = new Date().format('yyyyMMdd_hhmmss')
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def viash_config = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
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def version = get_version(viash_config)
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workflow run_wf {
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take:
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input_ch
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main:
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output_ch = input_ch
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| map { id, state ->
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// The argument names for this workflow and the demultiplex workflow may overlap
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// here, we store a copy in order to make sure to not accidentally overwrite the state.
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def new_state = state + [
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"fastq_output_workflow": state.fastq_output,
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"multiqc_output_workflow": state.multiqc_output,
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"sample_qc_output_workflow": state.sample_qc_output,
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"demultiplexer_logs_workflow": state.demultiplexer_logs,
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]
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return [id, new_state]
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}
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// Extract the ID from the input.
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// If the input is a tarball, strip the suffix.
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| map{ id, state ->
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def id_with_suffix = state.input.getFileName().toString()
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[
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id,
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state + [ run_id: id_with_suffix - ~/\.(tar.gz|tgz|tar)$/ ]
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]
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}
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| demultiplex.run(
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fromState: { id, state ->
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def state_to_pass = [
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"input": state.input,
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"run_information": state.run_information,
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"demultiplexer": state.demultiplexer,
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"skip_copycomplete_check": state.skip_copycomplete_check,
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"output": "$id/fastq",
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"output_sample_qc": "$id/qc/fastqc",
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"multiqc_output": "$id/qc/multiqc_report.html",
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"demultiplexer_logs": "$id/demultiplexer_logs",
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]
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if (state.run_information) {
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state_to_pass += ["output_run_information": state.run_information.getName()]
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}
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state_to_pass
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},
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toState: { id, result, state ->
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state + result
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},
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)
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| publish.run(
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fromState: { id, state ->
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println(state.plain_output)
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def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
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def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"
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def prefix = (id2 == "run") ? "" : "${id2}/"
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// These output names are determined by arguments.
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def fastq_output_1 = "${prefix}${state.fastq_output_workflow}"
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def sample_qc_output_1 = "${prefix}${state.sample_qc_output_workflow}"
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def multiqc_output_1 = "${prefix}${state.multiqc_output_workflow}"
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def demultiplexer_logs_output = "${prefix}${state.demultiplexer_logs_workflow}"
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// The name of the output file for the run information is determined by the input file name.
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def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
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println("Publising to ${params.publish_dir}/${prefix}")
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[
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input: state.output,
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input_sample_qc: state.output_sample_qc,
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input_multiqc: state.multiqc_output,
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input_run_information: state.output_run_information,
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input_demultiplexer_logs: state.demultiplexer_logs,
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output: fastq_output_1,
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output_sample_qc: sample_qc_output_1,
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output_multiqc: multiqc_output_1,
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output_run_information: run_information_output_1,
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output_demultiplexer_logs: demultiplexer_logs_output,
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]
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},
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toState: { id, result, state -> [:] },
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directives: [
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publishDir: [
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path: "${params.publish_dir}",
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overwrite: false,
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mode: "copy"
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]
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]
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)
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emit:
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output_ch
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}
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def get_version(input) {
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def inputFile = file(input)
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if (!inputFile.exists()) {
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// When executing tests
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return "unknown_version"
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}
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def yamlSlurper = new groovy.yaml.YamlSlurper()
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def loaded_viash_config = yamlSlurper.parse(inputFile)
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def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
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println("Version to be used: ${version}")
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return version
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}
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