genomic-medicine-sweden/gms_16s

A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.

gms_16s's Issues

Remove references to nf-core

Remove references according to https://nf-co.re/developers/tutorials/unofficial_pipelines

nanoplot creates the report for only one sample

The stats is not for all the samples in the batch. The report is only created for one sample.

Add Filtlong module

Already on nf-core. Import this or make a new module with e.g., nanofilt.

Switch from fastqc to falco module

Find a place to store all databases for emu so that users can download them.

Add log file for EMU module

EMU STDout should end up in a file since each sample will get some STDout on screen.
edit: E.g., unassigned read count, assigned read count, and em-iterations

Add module porechop_abi

I believe this is ready to use on nf-core as a module or subworkflow. Should be optional to use porechop_abi.

Addition of 18S/ITS identification

Versions to a file

Fix so that all tools are writing to versions.yml

Relative path + absolute path in command

Relative path is not working properly in the command.

Add support for pacbio and short reads.

check that the tools are working properly.

Test the tools too see that they do what they are supposed to.

Add visualizationfor the results.

The results from EMU is a .tsv file. Make the results more visual.