piRNA pipelines update
This issue is a reminder of the things I need to do for the final fixes of the smallRNA pipeline. Feel free to add comments it is will probably be relevant to me ;)
TODO:
-
Add filter structural RNAs - Add documentation:
-
for all 3 pipelines (sensor, small RNA Ce, piRNA zebrafish) -
add example output plots -
how to create the GTFs for small RNA classes (create script?)
-
-
Add small test data -
Make input / output filenames consistent with those of the other pipelines -
In filter_smRNA_classes.module.groovy
add size and first nucleotide as variables tofilter_smRNA_classes.vars.groovy
-
for the Zf piRNA sumnmary, remove plot dependency on file names. -
update the filter reads script for python3 -
tools.version
->pipeline
folder -
bpipe.config
-> newconfig
folder -
bug fix, long file names in output are not deteted as produced.
Edited by Antonio Domingues