Thiseas C. Lamnidis
Thiseas C. Lamnidis
PileupCaller module is required to avoid using local test data.
Preparing a PR that will be adding the option to include `--platypus` to the command. I cannot get `--first` to work. It seems that the latest pmdtools release lacks some...
https://github.com/pontussk/PMDtools/issues/8
# Using Conda ``` $ conda create --name pmdtools pmdtools -c bioconda` $ conda activate pmdtools ``` ```pmdtools --version pmdtools v0.50 ``` ``` $ samtools calmd -b JK2067_rmdup.bam hs37d5.fa |...
ok. They are currently migrating to nf-tests, so you could try to set up those instead of using pytest potentially.
Made some changes to skip using the input BAMs if they get converted, and tweaked spaces where output from the now-optional modules was used. Have another look just for completion.
Waiting for James to test specifically that the right reads from the BAM make it to the FastQs. Not updated the branch to make testing easier. James, once you are...
The issue with the config selector warning is something that has been "fixed" by the conventions we implemented in [dev_docs.md](https://github.com/nf-core/eager/blob/dev/docs/development/dev_docs.md). The point about making the ansi log shorter is still...
Addressed in #1016
Add mapAD? NOTE: Cheristian mentioned in his Lab Seminar on 11/09/2023 that the map quality calculation between mapAD and BWA is a bit different. Might be good to note that...