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remove 'auto' test

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This commit is contained in:
Mahesh Binzer-Panchal 2022-05-06 13:33:27 +00:00
parent 9fa6b6c1fc
commit 7a85760d08
2 changed files with 47 additions and 31 deletions
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48
tests/modules/busco/main.nf
View file

@ -13,12 +13,58 @@ workflow test_busco_genome_single_fasta {
BUSCO ( BUSCO (
input, input,
['auto','bacteria_odb10', 'bacteroidetes_odb10'], // Launch with auto to use --auto-lineage, and specified lineages ['bacteria_odb10', 'bacteroidetes_odb10'], // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
[], // Download busco lineage [], // Download busco lineage
[], // No config [], // No config
) )
/* Output tree: /* Output tree:
/tmp/tmpyz_hi62i/busco/
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.json
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.txt
├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.json
├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
├── test-bacteria_odb10-busco -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco/
│ ├── genome.fna/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── prodigal_err.log
│ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/
│ │ │ └── predicted_genes/
│ │ └── run_bacteria_odb10/
│ │ ├── busco_sequences/
│ │ ├── full_table.tsv
│ │ ├── hmmer_output/
│ │ ├── missing_busco_list.tsv
│ │ ├── short_summary.json
│ │ └── short_summary.txt
│ └── logs/
│ └── busco.log
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco.batch_summary.txt
├── test-bacteroidetes_odb10-busco -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco/
│ ├── genome.fna/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── prodigal_err.log
│ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/
│ │ │ └── predicted_genes/
│ │ └── run_bacteroidetes_odb10/
│ │ ├── busco_sequences/
│ │ ├── full_table.tsv
│ │ ├── hmmer_output/
│ │ ├── missing_busco_list.tsv
│ │ ├── short_summary.json
│ │ └── short_summary.txt
│ └── logs/
│ └── busco.log
├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
└── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
Former Output tree -w 'auto':
/tmp/tmp846crjv2/busco/ /tmp/tmp846crjv2/busco/
├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt

30
tests/modules/busco/test.yml
View file

@ -3,20 +3,6 @@
tags: tags:
- busco - busco
files: files:
- path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.txt
contains:
- "BUSCO version"
- "The lineage dataset is"
- "BUSCO was run in mode"
- "Complete BUSCOs"
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
contains: contains:
- "one_line_summary" - "one_line_summary"
@ -31,20 +17,6 @@
- "Complete BUSCOs" - "Complete BUSCOs"
- "Missing BUSCOs" - "Missing BUSCOs"
- "Dependencies and versions" - "Dependencies and versions"
- path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.txt
contains:
- "BUSCO version"
- "The lineage dataset is"
- "BUSCO was run in mode"
- "Complete BUSCOs"
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
contains: contains:
- "one_line_summary" - "one_line_summary"
@ -59,8 +31,6 @@
- "Complete BUSCOs" - "Complete BUSCOs"
- "Missing BUSCOs" - "Missing BUSCOs"
- "Dependencies and versions" - "Dependencies and versions"
- path: output/busco/test-auto-busco.batch_summary.txt
md5sum: 32f7765c310f33555c31c7a3e64c990e
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
md5sum: e50690742e9ae6abdd2bf99334ff9e12 md5sum: e50690742e9ae6abdd2bf99334ff9e12
- path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt