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Fix metaeuk_easypredict when using mmseqs database #3525

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Jul 12, 2023
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Fix metaeuk_easypredict when using mmseqs database #3525

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10 changes: 9 additions & 1 deletion modules/nf-core/metaeuk/easypredict/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,17 @@ process METAEUK_EASYPREDICT {
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
if [ -d ${database} ]; then
## if supplying an mmseqs database as a directory, metaeuk requires the basename of the database
DBBASE=`find ${database}/ -name "*.version" -exec sh -c 'file=\$(basename {}); echo \${file%%.*}' \\;`
DB=`echo "${database}/\${DBBASE}"`
else
DB=${database}
fi

metaeuk easy-predict \\
${fasta} \\
${database} \\
\${DB} \\
${prefix} \\
tmp/ \\
${args}
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25 changes: 21 additions & 4 deletions tests/modules/nf-core/metaeuk/easypredict/main.nf
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Expand Up @@ -2,18 +2,35 @@

nextflow.enable.dsl = 2

include { METAEUK_EASYPREDICT } from '../../../../../modules/nf-core/metaeuk/easypredict/main.nf'
include { MMSEQS_DATABASES } from '../../../../../modules/nf-core/mmseqs/databases/main.nf'
include { METAEUK_EASYPREDICT as METAEUK_EASYPREDICT_FASTA } from '../../../../../modules/nf-core/metaeuk/easypredict/main.nf'
include { METAEUK_EASYPREDICT as METAEUK_EASYPREDICT_MMSEQS } from '../../../../../modules/nf-core/metaeuk/easypredict/main.nf'

workflow test_metaeuk_easypredict {
workflow test_metaeuk_easypredict_fasta {

input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
]

database = [
fasta = [
file(params.test_data['proteomics']['database']['yeast_ups'], checkIfExists: true)
]

METAEUK_EASYPREDICT ( input, database )
METAEUK_EASYPREDICT_FASTA ( input, fasta )

}

workflow test_metaeuk_easypredict_mmseqs {

input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
]

MMSEQS_DATABASES ( 'UniProtKB/Swiss-Prot' )
database = MMSEQS_DATABASES.out.database

METAEUK_EASYPREDICT_MMSEQS ( input, database )

}
28 changes: 26 additions & 2 deletions tests/modules/nf-core/metaeuk/easypredict/test.yml
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@@ -1,5 +1,5 @@
- name: metaeuk easypredict test_metaeuk_easypredict
command: nextflow run ./tests/modules/nf-core/metaeuk/easypredict -entry test_metaeuk_easypredict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaeuk/easypredict/nextflow.config
- name: metaeuk easypredict test_metaeuk_easypredict_fasta
command: nextflow run ./tests/modules/nf-core/metaeuk/easypredict -entry test_metaeuk_easypredict_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaeuk/easypredict/nextflow.config
tags:
- metaeuk/easypredict
- metaeuk
Expand All @@ -13,3 +13,27 @@
- path: output/metaeuk/test.headersMap.tsv
md5sum: b3628c76d7385d326bd8a7931d974cff
- path: output/metaeuk/versions.yml

- name: metaeuk easypredict test_metaeuk_easypredict_mmseqs
command: nextflow run ./tests/modules/nf-core/metaeuk/easypredict -entry test_metaeuk_easypredict_mmseqs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaeuk/easypredict/nextflow.config
tags:
- metaeuk/easypredict
- metaeuk
files:
- path: output/metaeuk/test.codon.fas
- path: output/metaeuk/test.fas
- path: output/metaeuk/test.gff
- path: output/metaeuk/test.headersMap.tsv
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- path: output/metaeuk/versions.yml
- path: output/mmseqs/mmseqs_database/database
- path: output/mmseqs/mmseqs_database/database.dbtype
- path: output/mmseqs/mmseqs_database/database.index
- path: output/mmseqs/mmseqs_database/database.lookup
- path: output/mmseqs/mmseqs_database/database.source
- path: output/mmseqs/mmseqs_database/database.version
- path: output/mmseqs/mmseqs_database/database_h
- path: output/mmseqs/mmseqs_database/database_h.dbtype
- path: output/mmseqs/mmseqs_database/database_h.index
- path: output/mmseqs/mmseqs_database/database_mapping
- path: output/mmseqs/mmseqs_database/database_taxonomy
- path: output/mmseqs/versions.yml