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nf-core_modules/tests/modules/bclconvert/test.yml

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Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- name: bclconvert test_bclconvert
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>
2022-06-16 13:03:13 +00:00
command: nextflow run ./tests/modules/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config -c ./tests/modules/bclconvert/nextflow.config
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
tags:
- bclconvert
files:
- path: output/bclconvert/Logs/Errors.log
- path: output/bclconvert/Logs/FastqComplete.txt
- path: output/bclconvert/Logs/Info.log
- path: output/bclconvert/Logs/Warnings.log
Bump bcl-convert version (#2077) * Update main.nf * update test.yml * prettier
2022-09-16 12:34:52 +00:00
- path: output/bclconvert/Reports/Adapter_Cycle_Metrics.csv
md5sum: 5a0c88793b4a0885fe3dda16609b576e
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/Adapter_Metrics.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: 989240b8840b2169ac1061f952c90f6c
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/Demultiplex_Stats.csv
bump bclconvert version (#1806)
2022-06-24 05:14:42 +00:00
md5sum: 93949a8cd96f907d83e0808c1ec2a04b
Bump bcl-convert version (#2077) * Update main.nf * update test.yml * prettier
2022-09-16 12:34:52 +00:00
- path: output/bclconvert/Reports/Demultiplex_Tile_Stats.csv
md5sum: 83120160b0f22a1303fa1db31c19f6e9
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/IndexMetricsOut.bin
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>
2022-06-16 13:03:13 +00:00
md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/Index_Hopping_Counts.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: 1059369e375fd8f8423c0f6c934be978
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/Quality_Metrics.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: 6614accb1bb414fe312b17b81f5521f7
Bump bcl-convert version (#2077) * Update main.nf * update test.yml * prettier
2022-09-16 12:34:52 +00:00
- path: output/bclconvert/Reports/Quality_Tile_Metrics.csv
md5sum: cdc89fd2962bdd4a24f71e186112118a
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/RunInfo.xml
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>
2022-06-16 13:03:13 +00:00
md5sum: 03038959f4dd181c86bc97ae71fe270a
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/SampleSheet.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: dc0dffd39541dd6cc5b4801d768a8d2b
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: 2e2faba761137f228e56bd3428453ccc
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
- path: output/bclconvert/Reports/fastq_list.csv
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>
2022-06-16 13:03:13 +00:00
md5sum: 05bc84f51840f5754cfb8381b36f2cb0
- path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
Bump bcl-convert version (#2077) * Update main.nf * update test.yml * prettier
2022-09-16 12:34:52 +00:00
md5sum: 0a0341e2990b4fa1d9ad4b4c603144c1
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>
2022-06-16 13:03:13 +00:00
- path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
Bump bcl-convert version (#2077) * Update main.nf * update test.yml * prettier
2022-09-16 12:34:52 +00:00
md5sum: febef808ae5397ea4ee7ee40e5fd39e0
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>
2022-06-16 13:03:13 +00:00
- path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
md5sum: 6d77b38d0793a6e1ce1e85706e488953
- path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin
md5sum: 2bbf84d3be72734addaa2fe794711434
- path: output/bclconvert/flowcell/InterOp/ErrorMetricsOut.bin
md5sum: 38c88def138e9bb832539911affdb286
- path: output/bclconvert/flowcell/InterOp/ExtractionMetricsOut.bin
md5sum: 7497c3178837eea8f09350b5cd252e99
- path: output/bclconvert/flowcell/InterOp/IndexMetricsOut.bin
- path: output/bclconvert/flowcell/InterOp/QMetricsOut.bin
md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
- path: output/bclconvert/flowcell/InterOp/TileMetricsOut.bin
md5sum: 83891751ec1c91a425a524b476b6ca3c
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