config_ali

[bin_path]
binbase = /nfs/esnitkin/bin_group/assembly_bin/

[pbs]
resources: nodes=1:ppn=4,pmem=4000mb,walltime=250:00:00
large_resources: nodes=1:ppn=12,mem=47gb,walltime=250:00:00
email: apirani@med.umich.edu
queue: flux
flux_account: esnitkin
notification: a

[slurm]
resources: --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=5g --time=125:00:00
large_resources: --nodes=1 --ntasks-per-node=12 --mem=47000mb --time=250:00:00
email: apirani@med.umich.edu
partition: standard
flux_account: esnitkin1
notification: BEGIN,END,NONE,FAIL,REQUEUE

# Set which tools to use in pipeline:
[pipeline]
# Options for Aligner:bwa / smalt / bowtie
aligner: bowtie

[Trimmomatic]
trimmomatic_bin = /Trimmomatic/
#adaptor_filepath = adapters/NexteraPE-PE.fa
adaptor_filepath = adapters/TruSeq3-Nextera_PE_combined.fa
#adaptor_filepath = adapters/TruSeq3-PE.fa
adaptor_filepath_se = adapters/TruSeq3-SE.fa
seed_mismatches = 2
palindrome_clipthreshold = 30
simple_clipthreshold = 10
minadapterlength = 8
keep_both_reads = true
window_size = 4
window_size_quality = 20
minlength = 40
headcrop_length = 0
colon = :
targetlength = 125
crop_length = 40
f_p = /forward_paired.fq.gz
f_up = /forward_unpaired.fq.gz
r_p = /reverse_paired.fq.gz
r_up = /reverse_unpaired.fq.gz

[check_clean]
paired = 1
unpaired = 1

[spades]
spades_bin = /SPAdes-3.10.1-Linux/bin/
base_cmd = spades.py
threads = 
spades_parameters = --careful --sc
plasmid_spades_parameters = --plasmid
contigs_path = /spades_results/contigs.fasta
scaffolds_path = /spades_results/scaffolds.fasta
plasmid_contigs_path = /spades_plasmid_results/contigs.fasta
plasmid_scaffolds_path = /spades_plasmid_results/scaffolds.fasta

[bwa]
bwa_bin: /bwa-0.7.12/
cores: 8
base_cmd: bwa
algorithm: mem
index: index
RG_header: -R
Mark_splithits: -M

[bedtools]
bedtools_bin: //
base_cmd: bedtools
version_for_coverage: /version_for_coverage/

[bowtie]
bowtie_bin: /bowtie2-2.2.6/
cores: 8
build_cmd: bowtie2-build
align_cmd: bowtie2
parameters: --non-deterministic --end-to-end

[quast]
quast_bin = /quast/
base_cmd = quast.py
quast_parameters = --threads 8

[reapr]
reapr_bin = /Reapr_1.0.17/
base_cmd = reapr
reapr_parameters = 
perfectfrombam_parameters = perfect 100 500 3 4 76

[abacas]
abacas_bin = /PAGIT/ABACAS/
base_cmd = abacas.1.3.1.pl
abacas_parameters = -p nucmer -b -d -a -m

[mummer]
mummer_bin = /MUMmer3.23/

[prokka]
prokka_bin = /prokka-1.11/bin/
base_cmd = prokka
prokka_parameters = -kingdom Bacteria --force --rfam

[ariba]
ariba_bin = /nfs/esnitkin/bin_group/ariba/scripts/
base_cmd = ariba
ariba_amr_db = /nfs/esnitkin/bin_group/ariba/database/custom_new/out.card.proteus.prepareref/
ariba_mlst_db = /nfs/esnitkin/bin_group/ariba/database/MLST_db/Clostridium_difficile/ref_db/
#ariba_bin = /nfs/esnitkin/bin_group/anaconda3/bin/

#KPC MLST db
#ariba_mlst_db = /nfs/esnitkin/bin_group/ariba/database/MLST_db/KP_MLST/ref_db/
#Cdiff MLST db
#ariba_mlst_db = /nfs/esnitkin/bin_group/ariba/database/MLST_db/Clostridium_difficile/ref_db/

[bioawk]
bioawk_bin = /bioawk/
base_cmd = bioawk

[cd-hit]
cd_hit_bin = /nfs/esnitkin/bin_group/cd-hit/
base_cmd = cd-hit

[velvet]
velvet_bin = 
base_cmd = 
velvet_parameters = 
contigs_path = /velvet_results/contigs.fa
scaffolds_path = 

[XXXX]
ref_name = XXXX
ref_path = XXXX

[KPNIH1]
ref_name = KPNIH1.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPNIH1/

[MRSA_USA_300]
ref_name = MRSA_USA_300.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/MRSA_USA_300

[CDIFF_630]
ref_name = cdiff_630.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/CDIFF_630/

[CFT073]
ref_name = EcoliCFT073.fna
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/CFT073/

[paris]
ref_name = Paris.fna
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/paris/