dissectBCL.ini

[Dirs]
baseDir=/path/to/bcl/folder
outputDir=/path/to/fastq/output/folder
flowLogDir=/path/to/log/folder
seqFacDir=/path/to/share/qc/with/facility
piDir=/base/with/enduser/folders
bioinfoCoreDir=/path/to/share/qc/with/core
tempDir=/path/to/tempDir

[Internals]
PIs=[pi1,pi2,pi3,pi4,pi5]
seqDir=seqfolderstr
fex=False

[parkour]
user=parkourUser
password=parkourPw
cert=/path/to/cert.pem
URL=parkour.domain.tld

[software]
bclconvert=/path/to/bclconvert
fastqc_adapters=/path/to/fastqc_adapters.txt
kraken2db=/path/to/kraken2_contaminome/contaminomedb

[misc]
mpiImg=/path/to/multiqc_headerimg.jpg
krakenExpl="<font size="2"> Kraken is used to classify the reads and to detect contamination. <br> For this we use a *custom* database, with a simplified taxonomical hierarchy (that no longer resembles any true taxonomical classification. <br> In brief, by default we screen for: <li><b>eukaryotes</b> (human, mouse, fly, mosquito, lamprey, medaka, c-elegans, yeast, zebrafish and the moss-piglet)</li> <li><b>prokaryotes</b> (Ecoli, pseudomonas, mycoplasma and haemophilus influenza)</li> <li><b>viruses</b> (sars-cov2, influenza A,B & C, norwalk virus, rhinoviruses, drosophila C virus, phiX and lambda phage )</li> <li><b>custom databases</b> (ERCC spikes, univec core DB)</li> Note that for human, mouse, fly and mosquito we scan for mitochondrial and ribosomal contamination separately). <br> Only the top (most abundant) five hits and unclassified hits are shown, all other hits are grouped under an 'other' tag.</font>"   

[communication]
subject=dissectBCL
deepSeq=email@seqfacility.de
bioinfoCore=email@bioinfocore.de
fromAddress=sender@dissectbcl.de
host=hostmail.address.de