/
params.yml
78 lines (58 loc) · 2.56 KB
/
params.yml
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# How are the final results published?
# By default, files are copied from the work-dir.
# Valid settings: "copy", "move", "link", "symlink"
## Attention: "link" does not work on all filesystems, such as some /scratch volumes
publish_mode: "link"
# Where are the input files?
# The input file should be a comma-separated file with one line per sample,
# formatted in the following way:
# sampleID,reverse,forward
# Sample1,</path/to/raw/reads>/forward_reads.fastq.gz,</path/to/raw/reads>/reverse_reads.fastq.gz
samples: "/labs/asbhatt/data/bhatt_lab_sequencing/23-03-08_awigen2/all_samples.csv"
# Where should the results end up?
#### Attention: This should NOT be a relative path
#### Make it an absolute path so that you can use the different workflows
#### together.
outdir: "/labs/asbhatt/data/bhatt_lab_sequencing/23-03-08_awigen2/"
# Are you running this process on long-reads from ONT?
long_reads: false
#########################################################################
# Preprocessing parameters
# location of the host genome
# Important! It needs to be indexed already
host_genome_location: "/labs/asbhatt/data/databases/host_genomes/hg38/"
bwa_index_base: "hg38.fa"
# trim galore
trimgalore_quality: 30
trimgalore_min_read_length: 60
trimgalore_start_trim: 0
trimgalore_end_trim: 0
#########################################################################
# Classification parameters
run_motus: true
run_metaphlan: true
# parameters for mOTUs2
motus_map_mgs_cutoff: 2
motus_min_len_align_length: 75
motus_db_path: "/labs/asbhatt/data/databases/motus_db/3.0.3/db_mOTU/"
motus_gtdb_path: "/labs/asbhatt/data/databases/motus_db/3.0.3/mOTUs_3.0.0_GTDB_tax.tsv"
# parameters for metaphlan
metaphlan_db_path: "/labs/asbhatt/data/databases/metaphlan_db/vJan21/"
#########################################################################
# Assembly parameters
# bakta database
bakta_db_path: "/labs/asbhatt/data/databases/bakta_db/v_5.0/db/"
#########################################################################
# Binning parameters
# checkM database
checkm_db_path: "/labs/asbhatt/data/databases/checkm_db/2015_01_16/"
# path to the GTDB database
gtdb_db_path: "/labs/asbhatt/data/databases/GTDBTK/release214/"
#########################################################################
# Viral classification databases
# geNomad database
genomad_db_path: "/labs/asbhatt/data/databases/genomad/v1.6/genomad_db/"
# VIBRANT database
vibrant_db_path: "/labs/asbhatt/data/databases/vibrant_db/v1.2.1"
# CheckV database
checkv_db_path: "/labs/asbhatt/data/databases/checkv_db/checkv-db-v1.5"