CI
997c850d5f
Build pipeline: viash-hub.demultiplex.v0.4-m2h96
Source commit: cc1c33e8fe
Source message: Bump version to v0.4.1
96 lines
4.3 KiB
Plaintext
96 lines
4.3 KiB
Plaintext
workflow run_wf {
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take:
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input_ch // Channel with [id, state] pairs
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main:
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output_ch = input_ch
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// Gather input files from folder
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| map {id, state ->
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def newState = [:]
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println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
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// No auto-detection of run information file (it is user provided),
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// in this case the demultiplexer should also be specified.
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assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
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"you must also provide a demultiplexer"
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if (!state.run_information) {
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println("Run information was not specified, auto-detecting...")
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// The supported_platforms hashmap must be a 1-on-1 mapping
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// Also, it's keys must be present in the 'choices' field
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// for the 'run_information' argument in the viash config.
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def supported_platforms = [
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"bclconvert": "SampleSheet.csv", // Illumina
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"bases2fastq": "RunManifest.csv" // Element Biosciences
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]
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def found_sample_information = supported_platforms.collectEntries{demultiplexer, filename ->
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println("Checking if ${filename} can be found in input folder ${state.input}.")
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def resolved_filename = state.input.resolve(filename)
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if (!resolved_filename.isFile()) {
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resolved_filename = null
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}
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println("Result after looking for run information for ${demultiplexer}: ${resolved_filename}.")
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[demultiplexer, resolved_filename]
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}
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def demultiplexer = null
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def run_information = null
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found_sample_information.each{demultiplexer_candidate, file_path ->
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if (file_path) {
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// At this point, a candicate run information file was found.
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assert !run_information: "Autodetection of run information " +
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"(SampleSheet, RunManifest) failed: " +
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"multiple candidate files found in input folder. " +
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"Please specify one using --run_information."
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run_information = file_path
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demultiplexer = demultiplexer_candidate
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}
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}
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// When autodetecting, the run information should have been found
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assert run_information: "No run information file (SampleSheet, RunManifest) " +
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"found in input directory."
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// When autodetecting, the demultiplexer must be set if the run information was found
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assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
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"Please report this as a bug."
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// When autodetecting, the found demultiplexer must match
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// with the demultiplexer that the user has provided (in case it was provided).
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if (state.demultiplexer) {
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assert state.demultiplexer == demultiplexer,
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"Requested to use demultiplexer ${state.demultiplexer} " +
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"but demultiplexer based on the autodetected run information "
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"file ${run_information} seems to indicate that the demultiplexer "
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"should be ${demultiplexer}. Either avoid specifying the demultiplexer "
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"or override the autodetection of the run information by providing "
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"the file."
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}
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println("Using run information ${run_information} and demultiplexer ${demultiplexer}")
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// At this point, the autodetected state can override the user provided state.
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newState = newState + [
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"run_information": run_information,
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"demultiplexer": demultiplexer,
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]
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} // end auto-detection logic
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if (newState.demultiplexer in ["bclconvert"]) {
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// Do not add InterOp to state because we generate the summary csv's in the next
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// step based on the run dir, not the InterOp dir.
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def interop_dir = state.input.resolve("InterOp")
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assert interop_dir.isDirectory(): "Expected InterOp directory to be present."
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def copycomplete_file = state.input.resolve("CopyComplete.txt")
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assert (copycomplete_file.isFile() || state.skip_copycomplete_check):
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"'CopyComplete.txt' file was not found!"
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}
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def resultState = state + newState
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[id, resultState]
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}
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| setState(["demultiplexer_output": "demultiplexer",
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"run_information_output": "run_information"])
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emit:
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output_ch
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} |