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104 lines
2.3 KiB
Text
104 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BUSCO } from '../../../modules/busco/main.nf'
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workflow test_busco_genome_single_fasta {
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input = [
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[ id:'test' ], // meta map
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file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
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]
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BUSCO (
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input,
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'bacteria_odb10', // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
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[], // Download busco lineage
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[] // No config
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)
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}
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workflow test_busco_genome_multi_fasta {
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input = [
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[ id:'test' ], // meta map
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[
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file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
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file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
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]
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]
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BUSCO (
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input,
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'bacteria_odb10',
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[], // Download busco lineage
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[] // No config
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)
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}
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workflow test_busco_eukaryote_metaeuk {
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input = [
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[ id:'test' ], // meta map
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file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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]
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BUSCO (
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input,
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'eukaryota_odb10',
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[], // Download busco lineage
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[] // No config
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)
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}
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workflow test_busco_eukaryote_augustus {
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input = [
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[ id:'test' ], // meta map
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file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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]
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BUSCO (
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input,
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'eukaryota_odb10',
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[], // Download busco lineage
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[] // No config
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)
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}
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workflow test_busco_protein {
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input = [
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[ id:'test' ], // meta map
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file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
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]
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BUSCO (
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input,
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'bacteria_odb10',
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[], // Download busco lineage
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[] // No config
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)
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}
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workflow test_busco_transcriptome {
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input = [
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[ id:'test' ], // meta map
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file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
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]
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BUSCO (
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input,
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'bacteria_odb10',
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[], // Download busco lineage
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[] // No config
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)
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}
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