pipeline.config

basesh=`dirname $0`
pipeflag=`realpath ${basesh}/pipeline.flag`
. $pipeflag



##### input data #####
BASE=`readlink -f -q $FLAGS_base`
REF=`readlink -f -q $FLAGS_ref`
REFMMI=${REF%.*}.mmi
FAST5=`readlink -f -q $FLAGS_fast5`
FASTQSFOLD=`readlink -q -f $FLAGS_fastqs`
echo $REF $BASE 

##### 1 BASECALLING SETUP #####

#fastq
FASTQ=$BASE/$FLAGS_sample.fastq.gz

#dorado 
DORADOBAM_unsorted=$BASE/dorado/${FLAGS_sample}_unsorted_dorado.bam
DORADOBAM=$BASE/dorado/${FLAGS_sample}_dorado.bam




##### 2 MAPPING #####
#minimap2
MMI=$BASE/mmi
BAM=$MMI/${FLAGS_sample}_mmi.bam
DORADOMMI=$MMI/${FLAGS_sample}_dorado_mmi.bam




##### 3 VC #####
##### 3.1 SV #####

# sniffles
VCF_SNF=$BASE/vc/sniffles/${FLAGS_sample}_sniffles.vcf
NOQC_VCF_SNF=$BASE/vc/sniffles/noQC_${FLAGS_sample}_sniffles.vcf



##### 3.2 SMALL VARIANTS ##### 

# pmdv 

# Set up PMDV output directory
OUTPUT_DIR_PMDV="${BASE}/vc/pmdv"
PMDV_PREFIX="${FLAGS_sample}_pmdv"

# clair3
CLAIR_OUT="${BASE}/vc/clair3"