From 7a85760d080d74ea8b883f9255a6d3861fd7d44b Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 6 May 2022 13:33:27 +0000 Subject: [PATCH] remove 'auto' test --- tests/modules/busco/main.nf | 48 +++++++++++++++++++++++++++++++++++- tests/modules/busco/test.yml | 30 ---------------------- 2 files changed, 47 insertions(+), 31 deletions(-) diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf index e290b965..598e148a 100644 --- a/tests/modules/busco/main.nf +++ b/tests/modules/busco/main.nf @@ -13,12 +13,58 @@ workflow test_busco_genome_single_fasta { BUSCO ( 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 [], // No config ) /* 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/ ├── 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 diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml index 2a801e64..43b810ba 100644 --- a/tests/modules/busco/test.yml +++ b/tests/modules/busco/test.yml @@ -3,20 +3,6 @@ tags: - busco 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 contains: - "one_line_summary" @@ -31,20 +17,6 @@ - "Complete BUSCOs" - "Missing BUSCOs" - "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 contains: - "one_line_summary" @@ -59,8 +31,6 @@ - "Complete BUSCOs" - "Missing BUSCOs" - "Dependencies and versions" - - path: output/busco/test-auto-busco.batch_summary.txt - md5sum: 32f7765c310f33555c31c7a3e64c990e - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt md5sum: e50690742e9ae6abdd2bf99334ff9e12 - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt