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https://github.com/MillironX/nf-core_modules.git
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d16f1ea4d7
* add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
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 -c ./tests/modules/pirate/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: ["test1"]
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- path: output/pirate/results/binary_presence_absence.nwk
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md5sum: 1fcf7434911bbab39b74791259f1f989
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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/test1.co-ords.tab
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md5sum: f1e75c045b35bae260dadb1a2f000dfa
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- path: output/pirate/results/co-ords/test2.co-ords.tab
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md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
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- path: output/pirate/results/co-ords/test3.co-ords.tab
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md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
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- path: output/pirate/results/genome2loci.tab
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md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
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- path: output/pirate/results/genome_list.txt
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md5sum: c19ac63da7949b15179f42093cbf95b8
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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: ["test1_00242"]
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- path: output/pirate/results/loci_paralog_categories.tab
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md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
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- path: output/pirate/results/modified_gffs/test1.gff
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md5sum: 5dc220e472165c3b693e1017f38fc0e3
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- path: output/pirate/results/modified_gffs/test2.gff
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md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
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- path: output/pirate/results/modified_gffs/test3.gff
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md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
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- path: output/pirate/results/pan_sequences.fasta
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md5sum: 0492833706f0f969b49a3555c16ec40d
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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: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
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md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
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- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
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contains: ["test1_00081"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
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contains: ["test1_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: 6e483c773ed90bd50b33f2bd569343e4
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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: ["g0"]
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