update bclconvert module, as used in nf-core/demultiplex (#1569)
* update bclconvert module, as used in nf-core/demultiplex * reconfigure test with new test data * update test * formatting * update outputs, update meta * update module and test * update test config, test.yml * fix linting * emit logs and reports as dir * fix typo, recreate test.yml * fix linting Co-authored-by: CMGG ICT Team <ict@cmgg.be>master
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1ac223ad43
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@ -1,5 +1,14 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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withName: BCLCONVERT {
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ext.args = {[
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meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
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"--force",
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"--first-tile-only true"
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].join(" ").trim()}
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}
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withName: UNTAR {
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publishDir = [ enabled: false ]
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}
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}
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@ -1,52 +1,44 @@
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- name: bclconvert test_bclconvert
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command: nextflow run tests/modules/bclconvert -entry test_bclconvert -c tests/config/nextflow.config -stub-run
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command: nextflow run ./tests/modules/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config -c ./tests/modules/bclconvert/nextflow.config
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tags:
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- bclconvert
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files:
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- path: output/bclconvert/InterOp/InterOp.bin
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md5sum: d3dea0bb4ab1c8754af324f40b001481
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- path: output/bclconvert/Logs/Errors.log
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md5sum: 334645f09074b2597a692e395b716a9c
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- path: output/bclconvert/Logs/FastqComplete.txt
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md5sum: a4c4c6ce2d0de67d3b7ac7d1fcb512e4
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- path: output/bclconvert/Logs/Info.log
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md5sum: d238822d379f2277cac950ca986cb660
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- path: output/bclconvert/Logs/Warnings.log
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md5sum: aeefd2d631817e170f88f25ecaaf4664
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- path: output/bclconvert/Reports/Adapter_Metrics.csv
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md5sum: af62e9c7b44940cfd8ea11064a1f42ae
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md5sum: 989240b8840b2169ac1061f952c90f6c
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- path: output/bclconvert/Reports/Demultiplex_Stats.csv
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md5sum: d11313931fcaabb5ce159462ad3dd1da
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md5sum: bb2ed9c6b46e03fbc060efd2c75398b0
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- path: output/bclconvert/Reports/IndexMetricsOut.bin
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md5sum: 6bcee11c8145e3b1059ceaa91d2f5be7
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md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
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- path: output/bclconvert/Reports/Index_Hopping_Counts.csv
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md5sum: 697e40e0c0d48b4bd25f138ef60b0bde
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md5sum: 1059369e375fd8f8423c0f6c934be978
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- path: output/bclconvert/Reports/Quality_Metrics.csv
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md5sum: 3902fd38f6b01f1ce0f0e8724238f8f2
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md5sum: 6614accb1bb414fe312b17b81f5521f7
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- path: output/bclconvert/Reports/RunInfo.xml
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md5sum: 5bef7c7e76360231b0c4afdfc915fd44
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md5sum: 03038959f4dd181c86bc97ae71fe270a
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- path: output/bclconvert/Reports/SampleSheet.csv
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md5sum: c579e7d2c9c917c4cfb875a0373c0936
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md5sum: dc0dffd39541dd6cc5b4801d768a8d2b
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- path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
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md5sum: 39a5e7f6d21c12d6051afdc8261b6330
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md5sum: 2e2faba761137f228e56bd3428453ccc
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- path: output/bclconvert/Reports/fastq_list.csv
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md5sum: 32c51ab10e013fd547928de57361ffcb
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- path: output/bclconvert/sample1_S1_L001_R1_001.fastq.gz
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md5sum: 9b831a39755935333f86f167527a094d
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- path: output/bclconvert/sample1_S1_L001_R2_001.fastq.gz
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md5sum: 082f4f767b7619f409ca7e752ef482bf
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- path: output/bclconvert/sample1_S1_L002_R1_001.fastq.gz
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md5sum: 837764c89db93dfb53cd663c4f26f3d7
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- path: output/bclconvert/sample1_S1_L002_R2_001.fastq.gz
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md5sum: 1a42cf6ba0bb8fc7770f278e6d1ab676
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- path: output/bclconvert/sample2_S2_L001_R1_001.fastq.gz
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md5sum: 475bc426b7cc48d0551d40e31457dc78
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- path: output/bclconvert/sample2_S2_L001_R2_001.fastq.gz
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md5sum: f670ccd7d9352e0e67fe1c1232429d94
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- path: output/bclconvert/sample2_S2_L002_R1_001.fastq.gz
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md5sum: ebd5ff6fa5603e7d704b5a10598de58c
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- path: output/bclconvert/sample2_S2_L002_R2_001.fastq.gz
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md5sum: 2f83b460f52620d2548c7ef8845b31d7
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- path: output/stub/SampleSheet.csv
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md5sum: c579e7d2c9c917c4cfb875a0373c0936
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- path: output/bclconvert/versions.yml
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md5sum: 05bc84f51840f5754cfb8381b36f2cb0
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- path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
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md5sum: 883037281293a2ec4995d34257f19866
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- path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
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md5sum: a4745abc5e7fdb89cc6df3069f3c6e69
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- path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
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md5sum: 6d77b38d0793a6e1ce1e85706e488953
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- path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin
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md5sum: 2bbf84d3be72734addaa2fe794711434
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- path: output/bclconvert/flowcell/InterOp/ErrorMetricsOut.bin
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md5sum: 38c88def138e9bb832539911affdb286
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- path: output/bclconvert/flowcell/InterOp/ExtractionMetricsOut.bin
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md5sum: 7497c3178837eea8f09350b5cd252e99
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- path: output/bclconvert/flowcell/InterOp/IndexMetricsOut.bin
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- path: output/bclconvert/flowcell/InterOp/QMetricsOut.bin
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md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
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- path: output/bclconvert/flowcell/InterOp/TileMetricsOut.bin
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md5sum: 83891751ec1c91a425a524b476b6ca3c
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