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config.yaml.sample
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config.yaml.sample
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---
assemblies:
asm1:
reference: /path/to/reference1.fasta
genome_size: 20k
eukaryotic: False
long_read_paths:
- /path/to/long/read/file1.bam
- /path/to/long/read/fileN.bam
paired_short_read_paths:
- - /path/to/short/read/paired_file1.fq.gz
- /path/to/short/read/paired_file2.fq.gz
asm2:
name: assembly 2
reference: /path/to/reference2.fasta
genome_size: 20m
eukaryotic: False
long_read_paths:
- /path/to/long/read/file1.bam
- /path/to/long/read/fileN.bam
asmN:
genome_size: 10g
eukaryotic: True
long_read_paths:
- /path/to/long/read/file1.bam
- /path/to/long/read/fileN.bam
paired_short_read_paths:
- - /path/to/short/read/paired_file1_run1.fq.gz
- /path/to/short/read/paired_file2_run1.fq.gz
- - /path/to/short/read/paired_file1_run2.fq.gz
- /path/to/short/read/paired_file2_run2.fq.gz
paths:
smrtcmds_bin: /path/to/smrtcmds/bin
rules:
convert_long_reads:
resources:
mem_mb: 8000
raw_long_reads_qc:
resources:
mem_mb: 2000
initial_assembly:
resources:
cores: 16
mem_mb: 128000
map_long_reads_polish:
resources:
cores: 16
mem_mb: 64000
merge_long_read_alignments_polish:
resources:
cores: 4
mem_mb: 16000
sort_long_read_alignments_polish:
resources:
cores: 8
mem_mb: 32000
index_long_read_alignments_polish:
resources:
mem_mb: 4000
index_initial_assembly:
resources:
mem_mb: 4000
first_polish:
resources:
cores: 16
mem_mb: 64000
index_first_polish:
resources:
cores: 4
mem_mb: 16000
raw_short_reads_qc:
resources:
cores: 2
mem_mb: 8000
trim_short_reads:
resources:
cores: 4
mem_mb: 8000
params:
FASTQ_qual_format: "sanger"
min_3prime_end_qual: 30
min_mean_pretrim_read_qual: 30
min_trimmed_len: 60
trimmed_short_reads_qc:
resources:
cores: 2
mem_mb: 8000
map_short_reads_polish:
resources:
cores: 32
mem_mb: 128000
merge_short_read_alignments_polish:
resources:
cores: 4
mem_mb: 16000
sort_short_read_alignments_polish:
resources:
cores: 8
mem_mb: 32000
index_short_read_alignments_polish:
resources:
mem_mb: 8000
second_polish:
resources:
cores: 32
mem_mb: 256000
scaffolding:
resources:
cores: 24
mem_mb: 192000
params:
kmer_size: 19
order: "contigs"
assembly_comparison:
resources:
cores: 16
mem_mb: 64000