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