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New modules metabuli: Add- Build- Classify #5862

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New modules metabuli: Add- Build- Classify #5862

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d65991c
Initial script
TheOafidian Jun 5, 2023
92cb054
Initial meta
TheOafidian Jun 5, 2023
9666902
Module only accepts fasta
TheOafidian Jun 5, 2023
7a0d144
Start testing
TheOafidian Jun 6, 2023
85a8720
Local test succeeded
TheOafidian Jun 6, 2023
648b58e
Conditional gz
TheOafidian Jun 7, 2023
d2212c1
Replaced with minimal db
TheOafidian Jun 7, 2023
e4ea479
Add metabuli build
TheOafidian Jun 11, 2023
3947e0d
Add build module and tests
TheOafidian Jun 11, 2023
15cadac
Use modules branch of testdata
TheOafidian Jun 15, 2023
d36fb27
Build database from scratch
TheOafidian Jun 15, 2023
e839656
Adapt location test dumpfiles
TheOafidian Jun 21, 2023
c409189
Run stub for test
TheOafidian Jun 21, 2023
e67e9f2
Rewrite to use existing database
TheOafidian Jun 21, 2023
09815c8
Update paths and min memory needed
TheOafidian Jul 19, 2023
610cd6a
Merge branch 'metabuli' into master
TheOafidian Jun 17, 2024
8f30f74
init nf-test & add add module
Joon-Klaps Jun 21, 2024
f2f8ea9
furthere splitting up add & build
Joon-Klaps Jun 21, 2024
1b9d0ea
removing old pytest files
Joon-Klaps Jun 21, 2024
92aaf7f
testing setups metabuli - needs fixing
Joon-Klaps Jun 21, 2024
291c8a3
Merge branch 'master' into master
Joon-Klaps Jun 21, 2024
d159b8c
fix linting & resource requirements
Joon-Klaps Jul 3, 2024
b573997
Merge branch 'master' into master
Joon-Klaps Jul 26, 2024
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Use modules branch of testdata
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@TheOafidian
TheOafidian committed Jun 15, 2023
commit 15cadac7853f9addbb17f974623dc4c3075743d0
4 changes: 2 additions & 2 deletions tests/modules/nf-core/metabuli/build/main.nf
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Expand Up @@ -39,8 +39,8 @@ workflow test_metabuli_build {

genome = file("${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
dmp_files = [
file("${params.test_data_metabuli}/data/genomics/sarscov2/metagenome/names.dmp"),
file("${params.test_data_metabuli}/data/genomics/sarscov2/metagenome/nodes.dmp")
file("${params.test_data_base}/delete_me/metabuli/names.dmp"),
file("${params.test_data_base}/delete_me/metabuli/nodes.dmp")
]
acc2taxid = BUILD_ACC2TAXID(genome)
tax = CREATE_TAXONOMY_FOLDER(dmp_files)
Expand Down
9 changes: 2 additions & 7 deletions tests/modules/nf-core/metabuli/build/nextflow.config
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@@ -1,12 +1,7 @@
params {
test_data_metabuli = 'https://raw.githubusercontent.com/nf-core/test-datasets/metabuli'
}
process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withLabel:process_medium {
cpus = 6
memory = 36.GB
time = 8.h
memory = 6.5GB
}
}
}