slurm.yaml

__default__:
    time: "0-02:00:00"
    partition: "batch"
    qos: ""
    nodes: 1
    ntasks: 1
    explicit: ""
    job-name: "ONT_GDB.{rule}"

# Preprocessing
fastp_sr:
    time: "00-01:00:00"
    partition: "batch"

rm_rrna_bbmap:
    time: "00-4:00:00"
    partition: "batch"

rm_host_bbmap_sr_metat:
    time: "00-4:00:00"
    partition: "bigmem"

rm_host_bbmap_sr_metag:
    time: "00-4:00:00"
    partition: "bigmem"

rm_host_bbmap_lr_metag:
    time: "00-4:00:00"
    partition: "bigmem"

# Assembly
assembly_lr_flye:
    time: "00-8:00:00"
    partition: "bigmem"

assembly_lr_canu:
    time: "05-00:00:00"
    partition: "bigmem"
    qos: "--qos long"

assembly_sr_megahit:
    time: "01-4:00:00"
    partition: "bigmem"

assembly_sr_metaspades:
    time: "01-8:00:00"
    partition: "bigmem"

assembly_hy_metaspades:
    time: "01-12:00:00"
    partition: "bigmem"

assembly_hy_operams:
    time: "00-16:00:00"
    partition: "bigmem"

# Assembly polishing
polishing_racon_lr:
    time: "00-6:00:00"
    partition: "bigmem"

polishing_racon_sr:
    time: "00-6:00:00"
    partition: "bigmem"

polishing_medaka_lr:
    time: "01-00:00:00"
    partition: "bigmem"

# Mapping
mapping_bwa_idx_asm:
    time: "00-02:00:00"
    partition: "batch"

mapping_bwa_mem_asm_sr:
    time: "00-02:00:00"
    partition: "batch"

mapping_bwa_mem_asm_lr:
    time: "00-12:00:00"
    partition: "batch"

mapping_bwa_mem_asm_hy:
    time: "00-02:00:00"
    partition: "batch"

# Annotation
annotation_prodigal:
    time: "00-2:00:00"
    partition: "batch"

annotation_hmm_kegg:
    time: "00-8:00:00"
    partition: "batch"

annotation_plasflow:
    time: "00-01:00:00"
    partition: "bigmem"

# Analysis
analysis_mashmap_one2one:
    time: "00-00:30:00"
    partition: "batch"

analysis_diamond_db:
    time: "00-6:00:00"
    partition: "batch"

# Taxonomy
tax_kraken2_contigs:
    time: "00-00:30:00"
    partition: "bigmem"

tax_kraken2_sr:
    time: "00-00:30:00"
    partition: "bigmem"

tax_kraken2_lr:
    time: "00-00:30:00"
    partition: "bigmem"

tax_kaiju:
    time: "00-00:30:00"
    partition: "bigmem"

tax_kaiju_summary:
    time: "00-00:10:00"
    partition: "batch"