investigate filter function variable activation

count reads for fastq files also

Pipeline state used for initial benchmarking. (note: custom -c nf.con…

…fig file also used)

change mixcr output suffix, md5 substring

fix merge_starcounts tag

iotas in todo

fix lostcause code bug with 'text:' accession

remove nextflow config manifest entry for now

Remove star path from config

continue cgi adaption