Is your feature request related to a problem? Please describe.
Not a problem but a potential improvement. Currently, if we want QUAST to take reads into account during contig evaluation, they are being passed directly using the --i-reads flag. That results in QUAST mapping all the reads to the contigs, which increases the runtime significantly. QUAST allows passing a pre-generated alignment map using the --sam/--bam flags, which allows it to use the maps directly, without the need to align the reads first. We should expose this flag in our action so that a pre-generated map can be passed - we are usually generating it anyway as it is required for binning with MetaBAT.
Describe the solution you'd like
Expose the --bam flag from QUAST (in a form of --i-reads-to-contigs-map Q2 flag) to enable passing SampleData[AlignmentMap] to the action directly.
Is your feature request related to a problem? Please describe. Not a problem but a potential improvement. Currently, if we want QUAST to take reads into account during contig evaluation, they are being passed directly using the
--i-readsflag. That results in QUAST mapping all the reads to the contigs, which increases the runtime significantly. QUAST allows passing a pre-generated alignment map using the--sam/--bamflags, which allows it to use the maps directly, without the need to align the reads first. We should expose this flag in our action so that a pre-generated map can be passed - we are usually generating it anyway as it is required for binning with MetaBAT.Describe the solution you'd like Expose the
--bamflag from QUAST (in a form of--i-reads-to-contigs-mapQ2 flag) to enable passingSampleData[AlignmentMap]to the action directly.