Bracken allows user to get report on certain taxonomy level from a single kraken2 report via bracken -l LEVEL option. Introducing this feature into TaxProfiler can be useful.
TODO
New parameter bracken_level: a string of bracken supported level(s) separated by comma, eg: 'G,S,S1'
Params checking in lib/WorkflowTaxprofiler.groovy
Implant feature needs:
subworkflows/local/profiling.nf: ch_input_for_bracken to combine() level info then add to meta.bracken_level
subworkflows/local/standardisation_profiles.nf: ch_profiles_for_bracken to groupTuple() on different meta.bracken_level
Change params using and publishDir accordingly in conf/modules.config
Description of feature
Bracken allows user to get report on certain taxonomy level from a single kraken2 report via
bracken -l LEVEL
option. Introducing this feature into TaxProfiler can be useful.TODO
bracken_level
: a string of bracken supported level(s) separated by comma, eg:'G,S,S1'
lib/WorkflowTaxprofiler.groovy
subworkflows/local/profiling.nf
:ch_input_for_bracken
tocombine()
level info then add tometa.bracken_level
subworkflows/local/standardisation_profiles.nf
:ch_profiles_for_bracken
togroupTuple()
on differentmeta.bracken_level
conf/modules.config