Draft
Conversation
based on comments made in #8 (comment)
handle varscan iupac ambiguity codes
since the classify env is mixed conda-forge/bioconda while prc just uses conda-forge
remove non-zero exit code from 2vcf.py snakemake rule
explicit channel specifications
based on comments made in #8 (comment)
rebasing with master to obtain 2vcf.py fix
and redirect chatty stdout to a log file
A limit on the size of our datasets is that manta requires that there be at least 100 high-quality reads. So we can't go smaller than that.
…#14) also remove extra config params that nobody uses and mark some extra files as temp
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
...to endorse the use of mamba and offer a docker container for those who prefer it (see #8 (comment))