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Hi Christa,
Thank you for developing CelFiE. I am trying to run CelFiE on 2 samples (adult normal lung tissues-WGBS). After getting the coverage file from Bismark, I ran your prepare_bismark.sh scr…
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bash-4.2$ bio-fusion \
> -r1=$R1 \
> -r2=$R2 \
> -transcript=$transcript
I1104 12:57:44.433680 11841 main.go:336] Start reading geneDB
I1104 12:57:44.556241 11841 gene_db.go:310] Reading tran…
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Hello, Thank you for the great pipeline!
Now, I try to run the pipeline to call SV. I get an error when trying to run sv_pipeline.cwl, the error as below:
```Shell
cwltool /home/liuhui/ctDNA-pipeli…
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Command executed:
bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf
**java -jar -Xmx4g /Data/data/raja/cfdna/nextflo…
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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …
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Hi All,
Maybe I missed something but are there a command in snakemake file to specify a sample-paired normal control in the snakemake file? I successfully run once in tumor only mode.
Thanks.
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This is something I've been doing off-bcbio for quite a while and I think it would be worthwhile to streamline. I would like to use this issue to collect information on how people have been doing thei…
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@lh3 I was playing around with this tool but I couldn't get it to work on a "simple" case. I duplicated a read 100 times and would expect it to output the duplicated read. Any thoughts?
```
@M…
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## Bug Report
Similar to #1115 (now fixed), MergeBamAlignment breaks on non-paired input.
Input is a SAM file with both, paired and non-paired reads.
### Affected tool(s)
MergeBamAlignment
…
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@lindaxiang to fill in details
Got a request from Lincoln's group to run Alignment + Sanger pipelines through their data:
- data size is ~30TB for ~30 donors
- each donor has 1 normal + multiple tu…