env_options.txt

#Parameter default  match     [if experimental, what's affected]  # comments

PRODUCTION TRUE     FALSE                    # default: refuse experimental settings

CN         NKI      [A-Za-z0-9_.-]{2,10}     # Company name; readgroups and output name
BRCA_CLASS b1.191   (b1\.371|b1|b2)           # see README.md
TYPE       breast   ovarian
OUTCLS     cls      [A-Za-z0-9_.-]{2,10}     # output subdirectory for classification
TAG        -GRCh38-blacklist-merged -[A-Za-z0-9._-]+ #postfix for NKI_1m file

# keep mem below your system's or this may crash, `free -h' for what's available. At least 1G is required.
MEM        2G       [1-9][0-9]*G
PARALLEL   2        [1-9][0-9]{0,3}          # parallel * threads should be < CPU(s)
THREADS    4        [1-9][0-9]{0,3}          # ..but mind other users, same for MEM

DEBUG            FALSE     TRUE              # print executed commands

# The filename can differ, if checksum and fai match, the sequence and order of contigs is ok.
FASTA      Homo_sapiens.GRCh38.dna.primary_assembly.fa    [A-Za-z0-9_.-]{1,64}

#--[  EXPERIMENTAL options below, setting to non-default require PRODUCTION=FALSE  ]--#
SETM2C     FALSE     TRUE        classifier  # see README.md
CPFCOR     TRUE      FALSE       classifier  # crossplatform correction
PL         Illumina  [A-Za-z0-9_.-]{3,10} classifier  # supported platform; @RG
BLACKLIST  GRCh38-blacklist-merged.bed [A-Za-z0-9_.-]{1,256}\.bed classifier # blacklisted regions

KBIN_SIZE  20        [1-9][0-9]{0,3}      mappability
SEQLEN     65        [1-9][0-9]{0,3}      mappability
MINQUAL    15        [0-9]{1,2}           mappability

# if any of these change all bets are off..
CHROMINFO  /app/chromInfo.txt     /input/chromInfo.txt     pipeline
BINS       /app/windows-20k.txt   /input/windows-20k.txt   pipeline
GCCONT     /app/gccontent-20k.txt /input/gccontent-20k.txt pipeline
CHECKSUM   257604babc88d1a24bffa13f41c39172681c000a1dd396b32ebdcde0d1fa78f6 [a-f0-9]{64} pipeline