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Keiran Raine edited this page Oct 22, 2021 · 8 revisions

You need to construct archives emulating the following (the first element of the path within the archive is dropped in all cases):

For mapping:

# GRCh37d5
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/bwa_idx_GRCh37d5.tar.gz

# GRCh38
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/core_ref_GRCh38_hla_decoy_ebv.tar.gz
ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/bwa_idx_GRCh38_hla_decoy_ebv.tar.gz

FASTQ file name conventions

Paired fastq inputs require a common prefix and expected suffix to be paired correctly:

*_[12].fq[.gz]