CI
9868bb9100
Build pipeline: viash-hub.demultiplex.return-output-from-runner-rmgjr
Source commit: d853b212d5
Source message: Fix state
86 lines
3.9 KiB
Plaintext
86 lines
3.9 KiB
Plaintext
nextflow.enable.dsl=2
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include { gather_fastqs_and_validate } from params.rootDir + "/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
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workflow test_gather_and_validate {
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output_ch = Channel.fromList([
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[
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id: "run1",
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input: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/fastqs",
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sample_sheet: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/samplesheet.csv",
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]
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])
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| map { state -> [state.id, state]}
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| gather_fastqs_and_validate.run(toState: ["fastq_forward", "fastq_reverse"])
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output_ch
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| toSortedList{a, b -> a[0] <=> b[0]}
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| view {"Output: $it"}
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| map {
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assert it.size() == 3: "Expected three fastq pairs"
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def first_pair = it[0][1]
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assert first_pair.fastq_forward.collect{it.name} == ["Undetermined_S1_R1_001.fastq.gz"]
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assert first_pair.fastq_reverse.collect{it.name} == ["Undetermined_S1_R2_001.fastq.gz"]
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def second_pair = it[1][1]
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assert second_pair.fastq_forward.collect{it.name} == ["sample1_S1_L001_R1_001.fastq.gz", "sample1_S1_L002_R1_001.fastq.gz"]
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assert second_pair.fastq_reverse.collect{it.name} == ["sample1_S1_L001_R2_001.fastq.gz", "sample1_S1_L002_R2_001.fastq.gz"]
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def undetermined_pair = it[2][1]
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assert undetermined_pair.fastq_forward.collect{it.name} == ["sample2_S1_L001_R1_001.fastq.gz"]
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assert undetermined_pair.fastq_reverse.collect{it.name} == ["sample2_S1_L001_R2_001.fastq.gz"]
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}
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}
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workflow test_undetermined_empty {
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output_ch = Channel.fromList([
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[
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id: "run1",
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input: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/fastqs_undetermined_empty",
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sample_sheet: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/samplesheet.csv",
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]
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])
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| map { state -> [state.id, state]}
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| gather_fastqs_and_validate.run(toState: ["fastq_forward", "fastq_reverse"])
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output_ch
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| toSortedList{a, b -> a[0] <=> b[0]}
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| view {"Output: $it"}
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| map {
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assert it.size() == 3: "Expected three fastq pairs"
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def first_pair = it[0][1]
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assert first_pair.fastq_forward.collect{it.name} == ["Undetermined_S1_R1_001.fastq.gz"]
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assert first_pair.fastq_reverse.collect{it.name} == ["Undetermined_S1_R2_001.fastq.gz"]
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def second_pair = it[1][1]
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assert second_pair.fastq_forward.collect{it.name} == ["sample1_S1_L001_R1_001.fastq.gz", "sample1_S1_L002_R1_001.fastq.gz"]
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assert second_pair.fastq_reverse.collect{it.name} == ["sample1_S1_L001_R2_001.fastq.gz", "sample1_S1_L002_R2_001.fastq.gz"]
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def undetermined_pair = it[2][1]
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assert undetermined_pair.fastq_forward.collect{it.name} == ["sample2_S1_L001_R1_001.fastq.gz"]
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assert undetermined_pair.fastq_reverse.collect{it.name} == ["sample2_S1_L001_R2_001.fastq.gz"]
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}
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}
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workflow test_without_index {
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output_ch = Channel.fromList([
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[
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id: "run1",
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input: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/fastqs_undetermined_empty",
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sample_sheet: params.rootDir + "/src/dataflow/gather_fastqs_and_validate/test_data/samplesheet_no_index.csv",
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]
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])
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| map { state -> [state.id, state]}
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| gather_fastqs_and_validate.run(toState: ["fastq_forward", "fastq_reverse"])
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output_ch
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| toSortedList{a, b -> a[0] <=> b[0]}
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| view {"Output: $it"}
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| map {
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assert it.size() == 2: "Expected two fastq pairs"
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def first_pair = it[0][1]
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assert first_pair.fastq_forward.collect{it.name} == ["Undetermined_S1_R1_001.fastq.gz"]
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assert first_pair.fastq_reverse.collect{it.name} == ["Undetermined_S1_R2_001.fastq.gz"]
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}
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} |