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f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
39 lines
1.9 KiB
YAML
39 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: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
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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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