CI
1d3c6a62e0
Build pipeline: viash-hub.htrnaseq.fix-20-jv9qq
Source commit: 7ae6be67bd
Source message: Update CHANGELOG.md
74 lines
2.3 KiB
Plaintext
74 lines
2.3 KiB
Plaintext
workflow run_wf {
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take:
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input_ch
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main:
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pool_ch = input_ch
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| groupWells.run(
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fromState: [
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"input_r1": "input_r1",
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"input_r2": "input_r2",
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"well": "barcode",
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"pool": "pool",
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],
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toState: [
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"wells": "wells",
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"input_r1": "output_r1",
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"input_r2": "output_r2",
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]
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)
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| parallel_map.run(
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fromState: { id, state ->
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[
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"input_r1": state.input_r1,
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"input_r2": state.input_r2,
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"genomeDir": state.genomeDir,
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"barcodes": state.wells,
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"pool": state.pool,
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"wellBarcodesLength": 10,
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"umiLength": 10,
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"output": state.output,
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]
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},
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toState: ["output": "output"],
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directives: ["label": ["highmem", "lowcpu"]],
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)
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| setState(["output", "pool"])
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// input_ch is on pool level, while parallel_map
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// outputs multiple events per pool.
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// Join the results back to pool level
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input_join_ch = input_ch
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| map {id, state ->
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def newEvent = [state.pool, id, state]
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return newEvent
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}
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output_ch = input_join_ch.combine(pool_ch, by: 0)
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| map {pool, well_id, state_well, state_pool ->
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def well_output = state_pool.output.findAll{star_output_dir ->
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def barcodes_list = []
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// Get the barcode from the STAR file.
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// One STAR output contains the results for one
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// well barcode. We can look for the barcode in
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// the 'Solo.out/Gene/raw/barcode.tsv' file.
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def barcodes_files = files("${star_output_dir}/Solo.out/Gene/raw/barcodes.tsv")
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assert barcodes_files.size() == 1, \
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"Exactly one file should have matched the barcodes files (found: $barcodes_files)."
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def barcode
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barcodes_files.each{ it ->
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assert it.countLines() == 1,
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"Expected only one barcode in a single STAR output."
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barcode = it.text.trim()
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}
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return barcode == state_well.barcode
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}
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assert well_output.size() == 1, \
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"Two or more outputs from the mapping seemed to have processed barcode '$barcode'."
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[well_id, ["output": well_output[0]]]
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}
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emit:
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output_ch
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} |