samtools1.15.1220.05&2 &&
gzip -dc \$reffa > reference.fa &&
reffa="reference.fa" &&
samtools faidx \$reffa;
}
} &&
#end if
reffai=\$reffa.fai &&
#elif $addref_cond.addref_select == "cached":
## in case of cached the absolute path is used which allows to read
## a cram file without specifying the reference
reffa='${addref_cond.ref.fields.path}' &&
reffai=\$reffa.fai &&
#else
#set use_ref=False
#end if
]]>@HELP@@HELP@^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$10.1093/gigascience/giab008&1 | grep Version]]>