config.txt

EZMAP CONFIG FILE
>project-name=EzMapTest
>python3-path=/usr/bin/python3
>start-at-step=8
>aligner-to-use=hisat2
>user-email=

SLURM JOB MANAGER CONFIG OPTIONS
>slurm-account=dklab-research
>slurm-share=no
>slurm-partition=normal
>slurm-max-num-threads=4
>slurm-test-only=no

PRINSEQ CONFIG OPTIONS
>prinseq-path=cwd/tools/PRINSEQ/
>prinseq-min_qual_score=21
>prinseq-lc_method=dust
>prinseq-lc_threshold=7

BOWTIE2 CONFIG OPTIONS
>bowtie2-path=cwd/tools/BOWTIE2/bowtie2-2.2.5/
>bowtie2-index-path=cwd/tools/BOWTIE2/hg19/hg19

HISAT2 CONFIG OPTIONS
>hisat2-path=cwd/tools/HISAT2/hisat2-2.0.5-Linux/
>hisat2-index-path=cwd/tools/HISAT2/hg19-hisat/genome

SAMTOOLS CONFIG OPTIONS
>samtools-path=cwd/tools/SAMTOOLS/

BLAST CONFIG OPTIONS
>blast-path=cwd/tools/BLAST/ncbi-blast-2.4.0+/bin/
>blast-task=megablast
>blast-db-path=/mnt/hgfs/patrickczeczko/GithubRepos/ezmap/tools/BLAST/ncbi-blast-2.4.0+/db/viral.1.1.genomic.fna
>blast-dust=no
>blast-reward=1
>blast-penalty=-3
>blast-word_size=12
>blast-gapopen=5
>blast-gapextend=2
>blast-evalue=0.0001
>blast-culling_limit=2
>blast-perc_identity=90
>blast-min-alignment-length=45

EMAL CONFIG OPTIONS
>emal-path=cwd/tools/EMAL/
>emal-gi-taxid-nucldmp-path=/mnt/hgfs/patrickczeczko/GithubRepos/ezmap/tools/EMAL/gi_taxid_nucl.dmp
>emal-acceptance-value=0.0001

OUTPUT OPTIONS
- Options for this parameter are: SuperKingdom,Q1,Order,Family,SubFamily,Genus
>extraTableSummedOver=Family