Sam Nicholls
Sam Nicholls
The default installation environment for Clair3 uses Python 3.6.10 (https://github.com/HKU-BAL/Clair3/blob/main/Dockerfile#L25). Python 3.6 has reached end of life and has not received security updates since December 2021. Unless there are specific...
Adds a `-t ` option for `samtools merge` to create a tab-delimited text file in the format; ``` bam_filename @RG_ID Transformed_@RG_ID ``` eg. ``` /dat/test_input_1_b.bam fish PG:llama fish PG:llama /dat/test_input_1_b.bam...
**Version of Singularity** ``` $ singularity --version singularity-ce version 3.9.2 ``` **Describe the bug** When running a demo container I get the error: `container creation failed: failed to add as...
Clair3 packages [longphase 1.0](https://github.com/HKU-BAL/Clair3/blob/main/Makefile#L10), but we have been unable to use CRAM input with longphase < 1.3 due to a defect that was fixed [by this commit](https://github.com/twolinin/longphase/commit/5d450a3b7900271974a1610e73809cc3f12a60db). This requires us...
As briefly discussed in the nf-core Slack, I was recently asked by a user "how do I know what version I have of your workflow?" which seemed like a simple...
Although Gretel is not designed for recovering large haplotypes, it should at least try its best. Apparently very large contigs will cause Gretel to write very large temporary files and...
The docs website points to the old `snpper` script in the testing repository (which should perhaps be removed or archived given its age), rather than showing an invocation of `gretel-snpper`....
* [ ] Attempt to "ramp" the start of the target region by decreasing -s automatically * [ ] Minimal marginal aware reweighting * [ ] Reconsider approach for minimal...