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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.9 KiB
YAML
42 lines
1.9 KiB
YAML
- name: roary test_roary
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command: nextflow run ./tests/modules/roary -entry test_roary -c ./tests/config/nextflow.config -c ./tests/modules/roary/nextflow.config
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tags:
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- roary
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files:
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- path: output/roary/results/accessory.header.embl
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contains: ["ID Genome standard; DNA; PRO; 1234 BP."]
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- path: output/roary/results/accessory.tab
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contains: ["FT"]
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- path: output/roary/results/accessory_binary_genes.fa
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md5sum: d4191cf748dd8016ad877857a034bef3
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- path: output/roary/results/accessory_binary_genes.fa.newick
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md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea
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- path: output/roary/results/accessory_graph.dot
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contains: ["/* list of nodes */"]
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- path: output/roary/results/blast_identity_frequency.Rtab
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md5sum: 829baa25c3fad94b1af207265452a692
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- path: output/roary/results/clustered_proteins
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contains: ["JKHLNHAL_00087"]
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- path: output/roary/results/core_accessory.header.embl
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contains: ["ID Genome standard; DNA; PRO; 1234 BP."]
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- path: output/roary/results/core_accessory.tab
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contains: ['FT /taxa="test1 test2 test3"']
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- path: output/roary/results/core_accessory_graph.dot
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contains: ["/* list of nodes */"]
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- path: output/roary/results/gene_presence_absence.Rtab
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contains: ["Gene"]
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- path: output/roary/results/gene_presence_absence.csv
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contains:
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[
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'"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"',
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]
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- path: output/roary/results/number_of_conserved_genes.Rtab
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contains: ["279"]
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- path: output/roary/results/number_of_genes_in_pan_genome.Rtab
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contains: ["279"]
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- path: output/roary/results/number_of_new_genes.Rtab
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contains: ["279"]
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- path: output/roary/results/number_of_unique_genes.Rtab
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contains: ["279"]
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- path: output/roary/results/summary_statistics.txt
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md5sum: 3921b5445df6a7ed59408119b8860a58
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