mirror of
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053797510d
* new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
98 lines
5.1 KiB
YAML
98 lines
5.1 KiB
YAML
- name: pirate test_pirate
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command: nextflow run tests/modules/pirate -entry test_pirate -c tests/config/nextflow.config
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tags:
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- pirate
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files:
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- path: output/pirate/results/PIRATE.gene_families.ordered.tsv
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contains: ['allele_name']
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- path: output/pirate/results/PIRATE.gene_families.tsv
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contains: ['allele_name']
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- path: output/pirate/results/PIRATE.genomes_per_allele.tsv
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contains: ['g0197']
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- path: output/pirate/results/PIRATE.log
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contains: ['PIRATE input options']
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- path: output/pirate/results/PIRATE.pangenome_summary.txt
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md5sum: 4551c291bc06b21f984f25c09329ed7d
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- path: output/pirate/results/PIRATE.unique_alleles.tsv
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contains: ['allele_name']
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- path: output/pirate/results/binary_presence_absence.fasta
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contains: ['GCF_000292685']
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- path: output/pirate/results/binary_presence_absence.nwk
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md5sum: 5b5d86bf97d97de37bb9db514abb7762
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- path: output/pirate/results/cluster_alleles.tab
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contains: ['g0001']
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- path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
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md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
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- path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
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md5sum: a24d6048b3074242bb558c7fa27a8b03
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- path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
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md5sum: 0c08228585f4fa95686e9b025e0fe9c1
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- path: output/pirate/results/genome2loci.tab
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md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
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- path: output/pirate/results/genome_list.txt
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md5sum: 6534b1635c258ad92b829077addc1ff5
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- path: output/pirate/results/link_clusters.log
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contains: ['parsing paralog file']
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- path: output/pirate/results/loci_list.tab
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/loci_paralog_categories.tab
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md5sum: 6404d2a32526a398f42d7da768a389bd
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- path: output/pirate/results/modified_gffs/GCF_000292685.gff
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md5sum: 2b73bda2f84dc634303dc90e641040ca
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- path: output/pirate/results/modified_gffs/GCF_000298385.gff
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md5sum: b1a9d6557d47e09249f08a7acdbbd618
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- path: output/pirate/results/modified_gffs/GCF_002849995.gff
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md5sum: 68532fc9bb639e6d83c731a069f60cf8
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- path: output/pirate/results/pan_sequences.fasta
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md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
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- path: output/pirate/results/pangenome.connected_blocks.tsv
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contains: ['block_number']
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- path: output/pirate/results/pangenome.edges
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contains: ['g0259']
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- path: output/pirate/results/pangenome.gfa
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contains: ['g0001']
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- path: output/pirate/results/pangenome.order.tsv
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contains: ['g0172']
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- path: output/pirate/results/pangenome.reversed.tsv
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md5sum: b2396ce09a6e4178761eca6dc7f4434f
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- path: output/pirate/results/pangenome.syntenic_blocks.tsv
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contains: ['g0091']
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- path: output/pirate/results/pangenome.temp
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- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
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md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
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- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
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contains: ['GCF_000298385_00081']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
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contains: ['chaos']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
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md5sum: 84668b6c65b57026a17a50b0edd02541
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
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- path: output/pirate/results/pangenome_log.txt
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contains: ['Creating pangenome on amino acid']
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- path: output/pirate/results/paralog_clusters.tab
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contains: ['g0216']
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- path: output/pirate/results/representative_sequences.faa
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contains: ['representative_genome']
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- path: output/pirate/results/representative_sequences.ffn
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contains: ['representative_genome']
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- path: output/pirate/results/split_groups.log
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contains: ['g0213']
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