#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (c) 2021, Farid Rashidi Mehrabadi All rights reserved.

# ======================================================================================
# Author     : Farid Rashidi Mehrabadi (farid.rashidimehrabadi@nih.gov)
# Last Update: July 11, 2020
# Description: config file includes paths, directories, formats and parameters
#
# **NOTICE**:  for mouse: 'mmDBSNPs142' and 'mmDBIndels142'
#              for human: 'hgMillsIndels', 'hgKGIndels' and 'hgDBSNPs138'
# ======================================================================================

## PATHS
infq: "./trisicell/datasets/test/mcalling"
outdir: "./trisicell/datasets/test/_map"
tmpdir: "./trisicell/datasets/test/_tmp"
normals: [] # normal cells

## for paired-end
infqpre1: ""
infqpost1: "_1.fastq.gz"
infqpre2: ""
infqpost2: "_2.fastq.gz"

## for single-end
# infqpre: ""
# infqpost: ".fastq.gz"

## PARAMETERS
isrna: True
buildver: "mm10" #[mm10 for mouse | hg19 for human]
dotrimming: True
pairedend: True
email: "myemail@gmail.com"

## STEPS
steps:
  s01indexing: True # False by default when `isrna` False
  s02mapping: True
  s03indexing: True # False by default when `isrna` False
  s04mapping: True
  s05calling: True
  s06jointcalling: True
  s07merging: True
  s08annotating: True
  s09expressing: True # False by default when `isrna` False
  s10velocitying: True # False by default when `isrna` False

## TIME and MEM
mem01: "50"
time01: "02:00:00"

mem02: "90"
time02: "20:00:00"

mem03: "50"
time03: "02:00:00"

mem04: "100"
time04: "1-12:00:00"
java04: "java -Xmx90g -jar"

mem05: "100"
time05: "2-00:00:00"
java05: "java -Xmx90g -jar"

mem06: "100"
time06: "23:00:00"
java06: "java -Xmx90g -jar"
threads06: 16

mem07: "20"
time07: "02:00:00"

mem08: "20"
time08: "15:00:00"

mem09: "20"
time09: "15:00:00"

mem10: "100"
time10: "2-00:00:00"

## TOOLS
GATK: "/data/rashidimehrabf2/_software/GenomeAnalysisTK.jar" #version: 3.8-1-0-gf15c1c3ef
PICARD: "/data/rashidimehrabf2/_software/picard.jar" #version: 2.22.3
ANNOVAR: "/data/rashidimehrabf2/_software/annovar.2019.10.24" #version: 2019.10.24
BWA: "bwa" #version: 0.7.17
STAR: "STAR" #version: 2.7.3a
RSEM: "rsem" #version: 1.3.2
FASTQC: "fastqc" #version: 0.11.9
CUTADAPT: "cutadapt" #version: 2.9
TRIMGALORE: "trim_galore" #version: 0.6.5
TRIMMOMATIC: "trimmomatic" #version: 0.39
samtools: "samtools" #version: 1.11
bcftools: "bcftools" #version: 1.9
velocyto: "velocyto" #version: 0.17.17

## REFERENCES and INDICES
ref: "/data/rashidimehrabf2/_database/hg19/genome/GRCh37.p13.fa"
fdict: "/data/rashidimehrabf2/_database/hg19/genome/GRCh37.p13.dict"
annot: "/data/rashidimehrabf2/_database/hg19/annotation/gencode.v19.annotation.gtf"
rsemdb: "/data/rashidimehrabf2/_database/hg19/rsem/rsem"
whichdb: "humandb"
dbtype: "wgEncodeGencodeBasicV19"
velo: "/data/rashidimehrabf2/_database/hg19/velocyto/ucsc.v19.repeat_mask.gtf"

# ref: "/data/rashidimehrabf2/_database/mm10/genome/GRCm38.p6.fa"
# fdict: "/data/rashidimehrabf2/_database/mm10/genome/GRCm38.p6.dict"
# annot: "/data/rashidimehrabf2/_database/mm10/annotation/gencode.vM25.annotation.gtf"
# rsemdb: "/data/rashidimehrabf2/_database/mm10/rsem/rsem"
# whichdb: "mousedb"
# dbtype: "wgEncodeGencodeBasicVM25"
# velo: "/data/rashidimehrabf2/_database/mm10/velocyto/ucsc.vM25.repeat_mask.gtf"

## DB SNPS and INDELS
hgMillsIndels: "/data/rashidimehrabf2/_database/hg19/dbsnp/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz" #for human
hgKGIndels: "/data/rashidimehrabf2/_database/hg19/dbsnp/1000G_phase1.indels.hg19.sites.vcf.gz" #for human
hgDBSNPs138: "/data/rashidimehrabf2/_database/hg19/dbsnp/dbsnp_138.hg19.vcf.gz" #for human
mmDBSNPs142: "/data/rashidimehrabf2/_database/mm10/dbsnp/mgp.v5.merged.snps_all.dbSNP142.chr.vcf.gz" #for mouse
mmDBIndels142: "/data/rashidimehrabf2/_database/mm10/dbsnp/mgp.v5.merged.indels.dbSNP142.normed.chr.vcf.gz" #for mouse