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Update busco to v5.4.3 and tar small files (#1970)

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* Update busco to v5.4.3 and tar small files

* Fix file contain strings

* Swap md5sums to contains for variable files
This commit is contained in:
Mahesh Binzer-Panchal 2022-08-30 10:25:01 +02:00 committed by GitHub
parent bbb99cb8d6
commit 89a84538be
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 571 additions and 132 deletions
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6
modules/busco/main.nf
View file

@ -2,10 +2,10 @@ process BUSCO {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
conda (params.enable_conda ? "bioconda::busco=5.4.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"
input:
tuple val(meta), path('tmp_input/*')

90
tests/modules/busco/main.nf
View file

@ -15,7 +15,7 @@ workflow test_busco_genome_single_fasta {
input,
['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
[] // No config
)
/* Output tree:
@ -63,84 +63,6 @@ workflow test_busco_genome_single_fasta {
│ └── 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
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
│ ├── genome.fna/
│ │ ├── auto_lineage/
│ │ │ ├── run_archaea_odb10/
│ │ │ ├── run_bacteria_odb10/
│ │ │ └── run_eukaryota_odb10/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── metaeuk_err.log
│ │ │ ├── metaeuk_out.log
│ │ │ ├── prodigal_err.log
│ │ │ ├── prodigal_out.log
│ │ │ ├── sepp_err.log
│ │ │ └── sepp_out.log
│ │ ├── prodigal_output/
│ │ │ └── predicted_genes/
│ │ ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/ [recursive, not followed]
│ │ └── run_bacteroidales_odb10/
│ │ ├── busco_sequences/
│ │ ├── full_table.tsv
│ │ ├── hmmer_output/
│ │ ├── missing_busco_list.tsv
│ │ ├── short_summary.json
│ │ └── short_summary.txt
│ └── logs/
│ └── busco.log
├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/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/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/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/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
└── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
*/
}
@ -159,7 +81,7 @@ workflow test_busco_genome_multi_fasta {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)
/* Output tree:
@ -218,7 +140,7 @@ workflow test_busco_eukaryote_metaeuk {
input,
'eukaryota_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)
/* Output tree:
@ -259,7 +181,7 @@ workflow test_busco_eukaryote_augustus {
input,
'eukaryota_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)
/* Output tree:
@ -303,7 +225,7 @@ workflow test_busco_protein {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)
/* Output tree:
@ -339,7 +261,7 @@ workflow test_busco_transcriptome {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)
/* Output tree:

12
tests/modules/busco/nextflow.config
View file

@ -3,26 +3,26 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: 'test_busco_genome_single_fasta:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}
withName: 'test_busco_genome_multi_fasta:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}
withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}
withName: 'test_busco_eukaryote_augustus:BUSCO' {
ext.args = '--mode genome --augustus'
ext.args = '--mode genome --augustus --tar'
}
withName: 'test_busco_protein:BUSCO' {
ext.args = '--mode proteins'
ext.args = '--mode proteins --tar'
}
withName: 'test_busco_transcriptome:BUSCO'{
ext.args = '--mode transcriptome'
ext.args = '--mode transcriptome --tar'
}
}

595
tests/modules/busco/test.yml
View file

@ -1,12 +1,11 @@
- name: busco test_busco_genome_single_fasta
command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
@ -20,7 +19,6 @@
- path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
@ -32,21 +30,142 @@
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
md5sum: e50690742e9ae6abdd2bf99334ff9e12
md5sum: bc2440f8a68d7fbf931ff911c1c3fdfa
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
contains:
- "Tool: prodigal"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
md5sum: 275a7ece09ef61aa59ee7a811289e3d8
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
md5sum: ab574cde031a3fbff471976ea61e215d
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "lineage_dataset"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-bacteria_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
md5sum: 4c1b2c4317c88398eddc30877ed740d9
- path: output/busco/versions.yml
md5sum: 8aa830f71587d859df35c6cfab59f35d
md5sum: 5ad8ecfbf4058b059e5edeb9170fc683
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_err.log
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_err.log
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/.checkpoint
contains:
- "Tool: prodigal"
- "Completed"
- "jobs"
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/full_table.tsv
md5sum: 2360bb06f7171dafaa7ebf879789689b
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/hmmer_output.tar.gz
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/missing_busco_list.tsv
md5sum: e1fb12cf416448d35fbc5c508065963a
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "lineage_dataset"
- path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-bacteroidetes_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- name: busco test_busco_genome_multi_fasta
command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
@ -60,7 +179,6 @@
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
@ -74,28 +192,145 @@
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
contains:
- "Input_file"
- "Dataset"
- "Complete"
- "Single"
- "Duplicated"
- "Fragmented"
- "Missing"
- "n_markers"
- "genome.fasta"
- "genome.fna"
- "genome.fasta"
- "bacteria_odb10"
- path: output/busco/versions.yml
md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_err.log
md5sum: c1fdc6977332f53dfe7f632733bb4585
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_out.log
md5sum: 50752acb1c5a20be886bfdfc06635bcb
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/.checkpoint
contains:
- "Tool: prodigal"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.faa
md5sum: 8166471fc5f08c82fd5643ab42327f9d
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.fna
md5sum: ddc508a18f60e7f3314534df50cdf8ca
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
md5sum: 8166471fc5f08c82fd5643ab42327f9d
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
md5sum: ddc508a18f60e7f3314534df50cdf8ca
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
md5sum: c1fdc6977332f53dfe7f632733bb4585
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
md5sum: 50752acb1c5a20be886bfdfc06635bcb
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa
md5sum: e56fd59c38248dc21ac94355dca98121
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna
md5sum: b365f84bf99c68357952e0b98ed7ce42
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log
md5sum: e5f14d7925ba14a0f9850542f3739894
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log
md5sum: d41971bfc1b621d4ffd2633bc47017ea
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/full_table.tsv
md5sum: f473ded1f1db2463533d51be6ed6fd2d
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/missing_busco_list.tsv
md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "dataset"
- path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
contains:
- "Tool: prodigal"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
md5sum: 836e9a80d33d8b89168f07ddc13ee991
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
md5sum: 20eeb75f86842e6e136f02bca8b73a9f
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
md5sum: 538510cfc7483498210f01e53fe035ad
- path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
md5sum: 61050b0706addc9498b2088a2d6efa9a
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
md5sum: 275a7ece09ef61aa59ee7a811289e3d8
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
md5sum: ab574cde031a3fbff471976ea61e215d
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "dataset"
- path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-bacteria_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- name: busco test_busco_eukaryote_metaeuk
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
@ -107,29 +342,132 @@
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
md5sum: a70806f99ba5706d7353d3353b3f1d2b
- path: output/busco/versions.yml
md5sum: 34a808c257e6db1b0456f3b4372bc477
md5sum: ff6d8277e452a83ce9456bbee666feb6
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_out.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_out.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_out.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/full_table.tsv
md5sum: ff1b64c2adadcf9f0a954a19893e421b
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/hmmer_output.tar.gz
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/.checkpoint
contains:
- "Tool: metaeuk"
- "Completed"
- "jobs"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/combined_pred_proteins.fas
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.codon.fas
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.fas
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.gff
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.headersMap.tsv
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa
md5sum: d80b8fa4cb5ed0d47d63d6aa93635bc2
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.codon.fas
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.fas
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.gff
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.headersMap.tsv
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/missing_busco_list.tsv
md5sum: 6c17c7e06991db898b318b932d686406
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "dataset"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- name: busco test_busco_eukaryote_augustus
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
md5sum: 660393dd43cd6a093b952d4b8ad41e40
- path: output/busco/versions.yml
md5sum: 2caac915461410b16a1524ac064cd0df
md5sum: cdd3ffd590a778cdd2f0f367ee86eba7
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/.checkpoint
contains:
- "Tool: makeblastdb"
- "Completed"
- "jobs"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ndb
md5sum: 0d553c830656469211de113c5022f06d
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nhr
md5sum: 82396da5130a85faf6d454e2889a1d45
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nin
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.njs
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.not
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nsq
md5sum: 4bc119903ac72152363f47612645046a
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ntf
md5sum: de1250813f0c7affc6d12dac9d0fb6bb
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nto
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
contains:
- "IUPAC"
- "genome scaffold"
- "Coverage"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_out.log
contains:
- "Building a new DB"
- "Adding sequences from FASTA"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_err.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_out.log
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
contains:
- "Tool: bbtools"
- "Completed"
- "jobs"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/.checkpoint
contains:
- "Tool: tblastn"
- "Completed"
- "jobs"
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/coordinates.tsv
- path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/tblastn.tsv
contains:
- "TBLASTN"
- "BLAST processed"
- "queries"
- path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Running Augustus gene predictor"
- name: busco test_busco_protein
command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_protein -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
@ -141,19 +479,46 @@
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
- path: output/busco/versions.yml
md5sum: d7392261a57960a7e6aea609dce824f5
md5sum: 7a65e6cbb6c56a2ea4e739ae0aa3297d
- path: output/busco/test-bacteria_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_err.log
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/full_table.tsv
md5sum: 81e0e9a5897bb72fffbb1866779f6834
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/missing_busco_list.tsv
md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.json
contains:
- "one_line_summary"
- "mode"
- "dataset"
- path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- name: busco test_busco_transcriptome
command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
command: nextflow run ./tests/modules/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
tags:
- busco
files:
- path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
contains:
- "one_line_summary"
- "input_file"
- "mode"
- "dataset"
- path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
@ -165,6 +530,158 @@
- "Missing BUSCOs"
- "Dependencies and versions"
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
md5sum: 9a176cafe66ac0adca89dc34ad2be13f
- path: output/busco/versions.yml
md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1
md5sum: 46118ecf60d1b87d22b96d80f4f03632
- path: output/busco/test-bacteria_odb10-busco/logs/busco.log
contains:
- "DEBUG:busco.run_BUSCO"
- "Results from dataset"
- "how to cite BUSCO"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/.checkpoint
contains:
- "Tool: makeblastdb"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ndb
md5sum: 3788c017fe5e6f0f58224e9cdd21822b
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nhr
md5sum: 8ecd2ce392bb5e25ddbe1d85f879582e
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nin
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.njs
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.not
md5sum: 0c340e376c7e85d19f82ec1a833e6a6e
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nsq
md5sum: 532d5c0a7ea00fe95ca3c97cb3be6198
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ntf
md5sum: de1250813f0c7affc6d12dac9d0fb6bb
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nto
md5sum: ff74bd41f9cc9b011c63a32c4f7693bf
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_err.log
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_out.log
contains:
- "# hmmsearch :: search profile(s) against a sequence database"
- "# target sequence database:"
- "Internal pipeline statistics summary:"
- "[ok]"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_err.log
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_out.log
contains:
- "Building a new DB"
- "Adding sequences from FASTA"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_err.log
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_out.log
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/.checkpoint
contains:
- "Tool: tblastn"
- "Completed"
- "jobs"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/coordinates.tsv
md5sum: cc30eed321944af293452bdbcfc24292
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_101.temp
md5sum: 73e9c65fc83fedc58f57f09b08f08238
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contains:
- "TBLASTN"
- "BLAST processed"
- "queries"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
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- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
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md5sum: 14bb2d7788bd0aa547e4a99df6659f1e
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md5sum: 485902b7b62403985ee9f781e17b20ab
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contains:
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- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.txt
contains:
- "# BUSCO version is:"
- "Results:"
- "busco:"
- path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/single_copy_proteins.faa
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md5sum: a7cd1b13c9ef91c7ef4e31614166f197
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