LukaP

Make clear in the documentation that the batch command is also running "call"

4

In https://cnvkit.readthedocs.io/en/stable/pipeline.html#batch, a code example summarize the steps that the batch command runs, but forgets at least about the "call" aspect. This is a bit confusing when a file .call.cns...

incompatibility with using `rules.rulename.output` and importing snakefile as a module, using `use rule a from somemodule as a with...`

3

**Snakemake version** tested with : 8.10.8 7.32.3 **Describe the bug** I have a snakefile using the Rule object to reference outputs from previous rules. I have a second snakefile in...

Running TRUST4 with non-10X single-cell data, barcodes are in the RG:Z headers of fastq

6

I have fastq files for scDNA with barcodes extracted in the headers, in the RG:Z field. ``` @A01789:135:HLKCJDMXY:1:1101:1027:1047 RG:Z:CGTGCCTATTCGGACAGT TTAAATTGGTATCAGAAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATCCGGAAACAGGGGTCCCATCAAGGTTCAGTGGAA + FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFF:,FFFFF:FFFFFFF,F ``` Is there a way to use this...