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46 lines
2.0 KiB
Plaintext
46 lines
2.0 KiB
Plaintext
params {
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config_profile_name = 'Test PEP profile'
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config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_runmerging = true
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kraken2 = true
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run_bracken = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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run_motus = false
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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withName: MEGAN_RMA2INFO {
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maxForks = 1
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}
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}
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