You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
This is a major rewrite to make this pipeline harmonious with nf-core, update the tools used (Stacks 2.0, remove read-joining, etc). Also a few other points that have been on my wishlist for improving usability.
Write a tool to scrape the Stacks logfiles for useful stats
Others
Core pipeline tasks
Remove FLASH
Make a dockerfile. Is Stacks 2.0 on bioconda?
Write a python script to parse denovo stacks to get: coverage, raw # sample loci, catalog loci per sample, "shared" loci histogram. Parse process_radtags also?
Make a MultiQC configuration to import this data
Get publically available data from ENA. Make proper test data.
Make a MultiQC module for Stacks >= 2.0
Polish
Make a GH release
Documentation, documentation, documentation
Travis-CI
Python3 support for in silico digest helper script
Others -- Stretch goals
Think about what output files stacks should be creating by default.
Let the user specify which output files to create -- Nah the defaults are probably fine -- Nuh-uh we need more!
genepop
structure
Scripts for running the Stacks web UI -- It's been removed in v >= 2.0
Pick a set of “best practice” parameters for Stacks and run all of these.
Clearly report r80 statistic of each run, i.e # of polymorhic loci shared by at least 80% of individuals in the population -- http://doi.org/10.1111/2041-210X.12775
Support running Stacks with a reference genome
Support for premade population map file
Support for already processed reads (skipping trimming and process_reads)
Option to not output trimmed and/or processed fastq files
The text was updated successfully, but these errors were encountered:
This is built on https://github.com/remiolsen/NGI-RADseqQC
This is a major rewrite to make this pipeline harmonious with nf-core, update the tools used (Stacks 2.0, remove read-joining, etc). Also a few other points that have been on my wishlist for improving usability.
Main tasks
Write a tool to scrape the Stacks logfiles for useful statsCore pipeline tasks
Write a python script to parse denovo stacks to get: coverage, raw # sample loci, catalog loci per sample, "shared" loci histogram. Parse process_radtags also?Make a MultiQC configuration to import this dataPolish
Others -- Stretch goals
Let the user specify which output files to create--Nah the defaults are probably fine-- Nuh-uh we need more!Scripts for running the Stacks web UI-- It's been removed in v >= 2.0process_reads
)The text was updated successfully, but these errors were encountered: