export workflow fixes - Githubissues

abueg commented 2 years ago

[ ] move hifiasm GFAs to assembly_vgp_HiC_2.0/intermediates/
[ ] tarball the merylDB
[ ] move bionano GFAs to assembly_vgp_HiC_2.0/intermediates/
[ ] do not export bionano intermediate fasta (the concatenated s1)
[x] export bionano AGP
[x] salsa AGP is named incorrectly
[x] check which salsa AGP is being used
[ ] export the S2 gfas into assembly_vgp_HiC_2.0/intermediates/
[x] fix the S2 fasta export path (it is currently exporting as pri.asm, so they end up overwritten). they should be assembly_vgp_HiC_2.0/hap1.s2.fasta.gz, etc.
[ ] fix the S2 metadata problem when exporting (workflow generates unnecessary *.bam.bai files)

abueg commented 2 years ago

salsa version does not seem to have the option for original coordinate AGP? would be this in the latest salsa ver: -m yes -O -p yes i don't see the -O option in the xml

abueg commented 2 years ago

merylDB is tared, change the extension

abueg / iwc

export workflow fixes #1