v1.0

This release includes new features such as

Dynamic restarting of pipelines that have been partially completed.
--common_variants option to allow input of common variants or known variant loci in the form of a vcf such as one provided through 1kgenomes in our README
--skip_remap option to skip fastq generation, remapping, and retagging (not recommended without --common_variants but otherwise use at your own risk)

Singularity build here

wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=15znQ43q-_R3k04DmbGs3pka2FXvao4TS' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=15znQ43q-_R3k04DmbGs3pka2FXvao4TS" -O souporcell.sif && rm -rf /tmp/cookies.txt

common variant files here
GRCh38

wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=15s8zvIit2UO-2lnL2DnsL0YFoR3AWWRF' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=15s8zvIit2UO-2lnL2DnsL0YFoR3AWWRF" -O filtered_2p_1kgenomes_GRCh38.vcf && rm -rf /tmp/cookies.txt

and for hg19

wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1ICfIhpA4iGPEz_lAZf6RLMFQlrfgaskL' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1ICfIhpA4iGPEz_lAZf6RLMFQlrfgaskL" -O filtered_2p_1kgenomes_hg19.vcf && rm -rf /tmp/cookies.txt