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* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
85 lines
3.4 KiB
YAML
85 lines
3.4 KiB
YAML
# According to the issue https://github.com/fenderglass/Flye/issues/164
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# Some fluctuations are expected because of the heuristics
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# Here we check the that test.assembly_info.txt contains at least one contig
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- name: flye test_flye_pacbio_raw
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_raw -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config -stub-run
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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- name: flye test_flye_pacbio_corr
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_corr -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_pacbio_hifi
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_hifi -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_nano_raw
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_raw -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config -stub-run
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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- name: flye test_flye_nano_corr
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_corr -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_nano_hq
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_hq -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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