2022-01-27 14:36:18 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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2022-05-03 08:42:56 +00:00
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include { BUSCO } from '../../../modules/busco/main.nf'
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2022-01-27 14:36:18 +00:00
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2022-05-04 09:22:43 +00:00
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workflow test_busco_genome_single_fasta {
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input = [
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2022-05-06 11:48:21 +00:00
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[ id:'test' ], // meta map
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2022-05-04 09:22:43 +00:00
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file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
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]
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BUSCO (
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input,
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2022-05-06 11:48:21 +00:00
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['auto','bacteria_odb10', 'bacteroidetes_odb10'], // Launch with auto to use --auto-lineage, and specified lineages
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2022-05-04 09:22:43 +00:00
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[], // Download busco lineage
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[], // No config
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)
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/* Output tree:
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2022-05-06 11:48:21 +00:00
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/tmp/tmp846crjv2/busco/
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├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
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├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
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├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
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├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
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├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
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├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
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├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
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├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
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├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
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│ ├── genome.fna/
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│ │ ├── auto_lineage/
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│ │ │ ├── run_archaea_odb10/
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│ │ │ ├── run_bacteria_odb10/
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│ │ │ └── run_eukaryota_odb10/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── metaeuk_err.log
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│ │ │ ├── metaeuk_out.log
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│ │ │ ├── prodigal_err.log
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│ │ │ ├── prodigal_out.log
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│ │ │ ├── sepp_err.log
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│ │ │ └── sepp_out.log
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│ │ ├── prodigal_output/
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│ │ │ └── predicted_genes/
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│ │ ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/ [recursive, not followed]
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│ │ └── run_bacteroidales_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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│ └── logs/
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│ └── busco.log
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├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
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├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fna/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── prodigal_err.log
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│ │ │ └── prodigal_out.log
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│ │ ├── prodigal_output/
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│ │ │ └── predicted_genes/
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2022-05-04 11:52:42 +00:00
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│ │ └── run_bacteria_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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2022-05-04 09:22:43 +00:00
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│ └── logs/
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│ └── busco.log
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2022-05-06 11:48:21 +00:00
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├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
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├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fna/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── prodigal_err.log
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│ │ │ └── prodigal_out.log
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│ │ ├── prodigal_output/
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│ │ │ └── predicted_genes/
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2022-05-04 11:52:42 +00:00
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│ │ └── run_bacteroidetes_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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2022-05-04 09:22:43 +00:00
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│ └── logs/
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│ └── busco.log
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2022-05-06 11:48:21 +00:00
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├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
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└── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
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2022-05-04 09:22:43 +00:00
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*/
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}
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workflow test_busco_genome_multi_fasta {
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2022-05-03 08:42:56 +00:00
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input = [
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2022-05-06 11:48:21 +00:00
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[ id:'test' ], // meta map
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2022-05-03 13:26:49 +00:00
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[
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file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
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file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
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]
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2022-05-03 08:42:56 +00:00
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]
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BUSCO (
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input,
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'bacteria_odb10',
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[], // Download busco lineage
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[], // No config
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)
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2022-05-04 09:22:43 +00:00
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/* Output tree:
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2022-05-04 11:52:42 +00:00
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/tmp/tmpk19byek7/busco/
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├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json
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├── short_summary.specific.bacteria_odb10.genome.fasta.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.txt
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├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.json
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├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.txt
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├── test-bacteria_odb10-busco -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco/
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fasta/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── prodigal_err.log
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│ │ │ └── prodigal_out.log
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│ │ ├── prodigal_output/
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│ │ │ └── predicted_genes/
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2022-05-04 11:52:42 +00:00
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│ │ └── run_bacteria_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fna/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── prodigal_err.log
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│ │ │ └── prodigal_out.log
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│ │ ├── prodigal_output/
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│ │ │ └── predicted_genes/
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2022-05-04 11:52:42 +00:00
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│ │ └── run_bacteria_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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2022-05-04 09:22:43 +00:00
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│ └── logs/
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│ └── busco.log
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2022-05-04 11:52:42 +00:00
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├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco.batch_summary.txt
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└── versions.yml -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/versions.yml
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2022-05-04 09:22:43 +00:00
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*/
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}
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workflow test_busco_eukaryote_metaeuk {
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input = [
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2022-05-06 11:48:21 +00:00
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[ id:'test' ], // meta map
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2022-05-04 09:22:43 +00:00
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file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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]
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BUSCO (
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input,
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'eukaryota_odb10',
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[], // Download busco lineage
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[], // No config
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)
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/* Output tree:
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2022-05-04 11:52:42 +00:00
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/tmp/tmpeq4dsir5/busco/
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├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json
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├── short_summary.specific.eukaryota_odb10.genome.fasta.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.txt
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├── test-eukaryota_odb10-busco -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco/
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fasta/
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│ │ ├── logs/
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│ │ │ ├── hmmsearch_err.log
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│ │ │ ├── hmmsearch_out.log
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│ │ │ ├── metaeuk_err.log
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│ │ │ └── metaeuk_out.log
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2022-05-04 11:52:42 +00:00
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│ │ └── run_eukaryota_odb10/
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│ │ ├── busco_sequences/
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│ │ ├── full_table.tsv
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│ │ ├── hmmer_output/
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│ │ ├── metaeuk_output/
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│ │ ├── missing_busco_list.tsv
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│ │ ├── short_summary.json
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│ │ └── short_summary.txt
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2022-05-04 09:22:43 +00:00
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│ └── logs/
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│ └── busco.log
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2022-05-04 11:52:42 +00:00
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├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco.batch_summary.txt
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└── versions.yml -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/versions.yml
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2022-05-04 09:22:43 +00:00
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*/
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}
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workflow test_busco_eukaryote_augustus {
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input = [
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2022-05-06 11:48:21 +00:00
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[ id:'test' ], // meta map
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2022-05-04 09:22:43 +00:00
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file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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]
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BUSCO (
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input,
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'eukaryota_odb10',
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[], // Download busco lineage
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[], // No config
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)
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/* Output tree:
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2022-05-04 11:52:42 +00:00
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/tmp/tmp2xqaygjj/busco/
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├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/
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2022-05-04 09:22:43 +00:00
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│ ├── genome.fasta/
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│ │ ├── blast_db/
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│ │ │ ├── genome.fasta.ndb
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│ │ │ ├── genome.fasta.nhr
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│ │ │ ├── genome.fasta.nin
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│ │ │ ├── genome.fasta.not
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│ │ │ ├── genome.fasta.nsq
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│ │ │ ├── genome.fasta.ntf
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│ │ │ └── genome.fasta.nto
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│ │ ├── logs/
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│ │ │ ├── makeblastdb_err.log
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│ │ │ ├── makeblastdb_out.log
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│ │ │ ├── tblastn_err.log
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│ │ │ └── tblastn_out.log
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│ │ └── run_eukaryota_odb10/
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│ │ ├── augustus_output/
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│ │ ├── blast_output/
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│ │ ├── busco_sequences/
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│ │ └── hmmer_output/
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│ └── logs/
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│ └── busco.log
|
2022-05-04 11:52:42 +00:00
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├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco.batch_summary.txt
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└── versions.yml -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/versions.yml
|
2022-05-04 09:22:43 +00:00
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*/
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}
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workflow test_busco_protein {
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input = [
|
2022-05-06 11:48:21 +00:00
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[ id:'test' ], // meta map
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2022-05-04 09:22:43 +00:00
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file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
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]
|
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|
|
|
|
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|
BUSCO (
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|
input,
|
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|
'bacteria_odb10',
|
|
|
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[], // Download busco lineage
|
|
|
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|
[], // No config
|
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|
)
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|
/* Output tree:
|
2022-05-04 11:52:42 +00:00
|
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|
/tmp/tmpzwd5dn56/busco/
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|
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|
|
├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json
|
|
|
|
|
├── short_summary.specific.bacteria_odb10.proteome.fasta.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.txt
|
|
|
|
|
├── test-bacteria_odb10-busco -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco/
|
2022-05-04 09:22:43 +00:00
|
|
|
│ ├── logs/
|
|
|
|
|
│ │ └── busco.log
|
|
|
|
|
│ └── proteome.fasta/
|
|
|
|
|
│ ├── logs/
|
|
|
|
|
│ │ ├── hmmsearch_err.log
|
|
|
|
|
│ │ └── hmmsearch_out.log
|
2022-05-04 11:52:42 +00:00
|
|
|
│ └── run_bacteria_odb10/
|
|
|
|
|
│ ├── busco_sequences/
|
|
|
|
|
│ ├── full_table.tsv
|
|
|
|
|
│ ├── hmmer_output/
|
|
|
|
|
│ ├── missing_busco_list.tsv
|
|
|
|
|
│ ├── short_summary.json
|
|
|
|
|
│ └── short_summary.txt
|
|
|
|
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt
|
|
|
|
|
└── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml
|
2022-05-04 09:22:43 +00:00
|
|
|
*/
|
|
|
|
|
}
|
|
|
|
|
workflow test_busco_transcriptome {
|
|
|
|
|
|
|
|
|
|
input = [
|
2022-05-06 11:48:21 +00:00
|
|
|
[ id:'test' ], // meta map
|
2022-05-04 09:22:43 +00:00
|
|
|
file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
|
|
|
|
|
]
|
|
|
|
|
|
|
|
|
|
BUSCO (
|
|
|
|
|
input,
|
|
|
|
|
'bacteria_odb10',
|
|
|
|
|
[], // Download busco lineage
|
|
|
|
|
[], // No config
|
|
|
|
|
)
|
|
|
|
|
|
|
|
|
|
/* Output tree:
|
2022-05-04 11:52:42 +00:00
|
|
|
/tmp/tmpitjyvo9g/busco/
|
|
|
|
|
├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
|
|
|
|
|
├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
|
|
|
|
|
├── test-bacteria_odb10-busco -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco/
|
2022-05-04 09:22:43 +00:00
|
|
|
│ ├── logs/
|
|
|
|
|
│ │ └── busco.log
|
|
|
|
|
│ └── test1.contigs.fa/
|
|
|
|
|
│ ├── blast_db/
|
|
|
|
|
│ │ ├── test1.contigs.fa.ndb
|
|
|
|
|
│ │ ├── test1.contigs.fa.nhr
|
|
|
|
|
│ │ ├── test1.contigs.fa.nin
|
|
|
|
|
│ │ ├── test1.contigs.fa.not
|
|
|
|
|
│ │ ├── test1.contigs.fa.nsq
|
|
|
|
|
│ │ ├── test1.contigs.fa.ntf
|
|
|
|
|
│ │ └── test1.contigs.fa.nto
|
|
|
|
|
│ ├── logs/
|
|
|
|
|
│ │ ├── hmmsearch_err.log
|
|
|
|
|
│ │ ├── hmmsearch_out.log
|
|
|
|
|
│ │ ├── makeblastdb_err.log
|
|
|
|
|
│ │ ├── makeblastdb_out.log
|
|
|
|
|
│ │ ├── tblastn_err.log
|
|
|
|
|
│ │ └── tblastn_out.log
|
|
|
|
|
│ ├── run_bacteria_odb10/
|
|
|
|
|
│ │ ├── blast_output/
|
|
|
|
|
│ │ ├── busco_sequences/
|
|
|
|
|
│ │ ├── full_table.tsv
|
|
|
|
|
│ │ ├── hmmer_output/
|
|
|
|
|
│ │ ├── missing_busco_list.tsv
|
|
|
|
|
│ │ ├── short_summary.json
|
|
|
|
|
│ │ ├── short_summary.txt
|
|
|
|
|
│ │ └── single_copy_proteins.faa
|
|
|
|
|
│ └── translated_proteins/
|
|
|
|
|
│ ├── 1024388at2.faa
|
|
|
|
|
│ ├── 1054741at2.faa
|
|
|
|
|
│ ├── 1093223at2.faa
|
|
|
|
|
│ ├── 1151822at2.faa
|
|
|
|
|
│ ├── 143460at2.faa
|
|
|
|
|
│ ├── 1491686at2.faa
|
|
|
|
|
│ ├── 1504821at2.faa
|
|
|
|
|
│ ├── 1574817at2.faa
|
|
|
|
|
│ ├── 1592033at2.faa
|
|
|
|
|
│ ├── 1623045at2.faa
|
|
|
|
|
│ ├── 1661836at2.faa
|
|
|
|
|
│ ├── 1674344at2.faa
|
|
|
|
|
│ ├── 1698718at2.faa
|
|
|
|
|
│ ├── 1990650at2.faa
|
|
|
|
|
│ ├── 223233at2.faa
|
|
|
|
|
│ ├── 402899at2.faa
|
|
|
|
|
│ ├── 505485at2.faa
|
|
|
|
|
│ ├── 665824at2.faa
|
|
|
|
|
│ ├── 776861at2.faa
|
|
|
|
|
│ ├── 874197at2.faa
|
|
|
|
|
│ ├── 932854at2.faa
|
|
|
|
|
│ └── 95696at2.faa
|
2022-05-04 11:52:42 +00:00
|
|
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco.batch_summary.txt
|
|
|
|
|
└── versions.yml -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/versions.yml
|
2022-05-04 09:22:43 +00:00
|
|
|
*/
|
|
|
|
|
|
2022-01-27 14:36:18 +00:00
|
|
|
}
|
