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New modules metabuli: Add- Build- Classify #5862

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Update paths and min memory needed
  • Loading branch information
TheOafidian committed Jul 19, 2023
commit 09815c8157b48bf92bdba23c4162830fb1e1bffe
23 changes: 5 additions & 18 deletions tests/modules/nf-core/metabuli/build/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,6 @@ nextflow.enable.dsl = 2

include { METABULI_BUILD } from '../../../../../modules/nf-core/metabuli/build/main.nf'

process BUILD_ACC2TAXID {
input:
path(genomes)
output:
path(acc2taxid)

script:
"""
echo -e "accession\taccession.version\ttaxid\tgi" > acc2taxid
accessionv=\$(cat ${genomes} | head -n1 |
cut -d " " -f1 | sed 's/>//')
echo -e "\${accessionv%.*}\t\$accessionv\t2697049\t111" >> acc2taxid
"""
}

process CREATE_TAXONOMY_FOLDER{
input:
path(dmpfiles)
Expand All @@ -38,11 +23,13 @@ process CREATE_TAXONOMY_FOLDER{
workflow test_metabuli_build {

genome = file("${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)

dmp_files = [
file("${params.test_data_base}/data/delete_me/metabuli/names.dmp"),
file("${params.test_data_base}/data/delete_me/metabuli/nodes.dmp")
file("${params.test_data_base}/data/delete_me/metabuli/taxonomy/names.dmp"),
file("${params.test_data_base}/data/delete_me/metabuli/taxonomy/nodes.dmp")
]
acc2taxid = BUILD_ACC2TAXID(genome)
acc2taxid = file("${params.test_data_base}/data/delete_me/metabuli/acc2taxid")

tax = CREATE_TAXONOMY_FOLDER(dmp_files)
METABULI_BUILD ( genome, acc2taxid, tax )
}
3 changes: 2 additions & 1 deletion tests/modules/nf-core/metabuli/build/nextflow.config
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

memory = "16GB"

}