Charlotte Capitanchik

error runing epinano_variants.py

4

Hi, When trying to run Epinano v1.2.0 variants.py with the following command: ``` python3 Epinano_Variants.py -R /bucket/LuscombeU/common/Breakpoints/Genomes/OSKA2016v1.9.fa \ -b /home/c/c-capitanchik/flash/osaka_direct_rna/MOP2/mop_preprocess/osdirna_results/alignment/pass_s.bam \ -s /bucket/.deigo/LuscombeU/live/charlottecapitanchik/software/jvarkit/dist/sam2tsv.jar \ -n 8 \ -T g ```...

Error in demultiplex.py with 3' barcode

1

"Handle the case where randomer is already in the header." This did not include if the nucleotide after the rbc is an N, which it often is, meaning that you...

Any chance of making a Conda package?

9

Any chance of packaging this up for Bioconda? would make containerising + Nextflow stuff so much easier!! Program is working so great I want it in my pipelines!

example of local_samples.tsv

3

I can't find an example of local_samples.tsv?

Allow index format specification in samtools view

23

adding an option so that if write_indexes is used the user can choose what index type they want generated. ## PR checklist Closes #XXX - [x] This comment contains a...

## Is your feature request related to a problem? Please describe ## Describe the solution you'd like ## Describe alternatives you've considered ## Additional context

## Is your feature request related to a problem? Please describe ## Describe the solution you'd like ## Describe alternatives you've considered ## Additional context