Jennifer Chang

Feature Request: standard input

2

Might be nice to accept standard input if the function takes a single argument, or use '-' to stand in for standard in?

### Description of proposed changes: Update annotations up to August 9th, 2022. Let me know if I missed anything. Otherwise, I move to merge this Thursday morning, after the current...

### Description of proposed changes: Update annotations up to September 30th, 2022. Let me know if I missed anything. ### Related Issue(s): Related to https://github.com/nextstrain/ncov-ingest/pull/348

## Description of proposed changes * Copy the nextclade_cache instead of moving, to preserve older caches While updating our cache on Terra, realized we may want to preserve older caches....

## Description In order to document and test the Terra WDL workflows, this issue outlines a somewhat major overhaul of WDL code. To stop maintaining 3 separate GitHub branches for...

## Description of proposed changes Since occasional questions about our Terra workflows have been raised during office hours or via DM's, the goal is to update documentation of 3 WDL...

DRAFT: add 'gene' feature capture when reading genbank files

1

## Description of proposed changes In response to https://github.com/nextstrain/rsv/pull/55#discussion_r1518248004, adds a 'gene' feature capture when reading GenBank files. Please feel free to commit changes to this branch, this initial commit...

Replace picard commands with GATK commands

1

## Description As [Picard has been incorporated into GATK from GATK4 onwards](https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4#:~:text=Starting%20with%20version%204.0%2C%20GATK,available%20from%20within%20GATK%20itself.), this is a rough substitution of picard commands with GATK commands. It's crucial to note that these modifications...

The [GATK Best Practices Workflow for DNA-Seq tutorial](https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.html#gsc.tab=0) currently presents information that may require an update. It is important to note that [Picard is included in GATK starting with GATK4](https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4#:~:text=Starting%20with%20version%204.0%2C%20GATK,available%20from%20within%20GATK%20itself.)....

Require PacBio CLR data to be bam files

1

If PacBio data is passed in as a fasta file, the `@RG` annotation is lost, and Arrow gccp will complain ``` gcpp ERROR: [pbbam] read group ERROR: basecaller version is...