Jake VanCampen

Fails with uninformative error

15

When running with the command: `./TRUST4/run-trust4 --od ./trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/*_R2_*.fastq.gz --barcode data/*_R1_*.fastq.gz --barcodeRange 0 15 + --UMI data/*_R1_*.fastq.gz --umiRange 16 25 + --repseq --barcodeWhitelist...

Hi, I am wondering if the counts reported in the THOR output file "-diffpeaks.bed" are reporting the number of reads for each replicate that overlap that peak, or if they...

Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

Complete Azure Batch SDK service clients

6

### Service Package Request Older versions of the Batch API that appear to be deprecated now in favor of armbatch have clients and associated methods for Pool, Job and Task....

fix: pip deployment path

2

- Fixes pip deployment import path in spawn_jobs.py because PIP_DEPLOYMENT_PATH was moved to snakemake/__init__.py in #3056 ### QC * [ ] The PR contains a test case for the changes...

Consider supporting docker engine along with appraiser as --sdm option

1

**Is your feature request related to a problem? Please describe.** The installation and usage of singularity can be kind of esoteric in comparison to the usage of docker for running...

Remote report generation

2

**Is your feature request related to a problem? Please describe.** - Would like to be able to generate reports to the default storage provider **Describe the solution you'd like** -...

feat: Convert to src layout with poetry and setuptools-scm and pixi

1

## Summary by CodeRabbit - **New Features** - Improved package metadata handling with a fallback mechanism for version information. - **Bug Fixes** - Enhanced compatibility for file copying operations across...

→snakedeploy -h Traceback (most recent call last): File "/miniforge3/envs/snakedeploy/bin/snakedeploy", line 5, in from snakedeploy.client import main File "/miniforge3/envs/snakedeploy/lib/python3.13/site-packages/snakedeploy/client.py", line 13, in from snakedeploy.deploy import deploy File "/miniforge3/envs/snakedeploy/lib/python3.13/site-packages/snakedeploy/deploy.py", line 11, in...

feat: only multi param trailing comma

2

This PR resolves #24 ## Summary by CodeRabbit - **Bug Fixes** - Improved parameter list formatting so that extra commas now appear only when multiple parameters are provided, ensuring clearer...