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### Description of feature
Could be good to do whatever can be done when we release to help prepare for validation.
I'm thinking benchmarking, GiAB, checking results...
Could be interesting to talk…
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This serves to hopefully set the infrastructure to a fully conda-based installation, making it easier for people to get started with PoolParty2. The bioconda recipe has two parts:
1. The `meta.yaml` …
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I think we need to revisit our trimming parameters for ThruPlex NGS16S libraries (more an issue for the clampi pipeline than this one). If it's straightforward to do, it might be helpful to preserve t…
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I have 2 following steps in CWL workflow that are executed conditionally (using when statement) and output from one of them is input for the second one, and second one contains scatter. There is a fra…
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**I used following commands to prepare the reference genome**
```
rsem-prepare-reference --gtf ref/Homo_sapiens.GRCh37.69.gtf \
--bowtie2 --bowtie2-path /home/ngs/bin/bowtie2 \
ref/Homo_…
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Hi There,
I got following issues when I was trying to run the program:
```
fasta=/data1/workspace/DCI/Kirsch/Jianguo.Huang/circRNA/bwaindex/genome.fa
gtf=/data1/Annotation/iGenome/Mus_musculus/U…
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Hello Developers,
I have been utilizing yahs for Hi-C data processing followed by Juicer's preprocessing pipeline. My command for running yahs was:
```bash
yahs /NGS/Fungi/Rc/juicer/references/…
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Thanks for developing this nice pipeline. I'm trying to use it for WGS data.
In the wiki page (https://github.com/cbg-ethz/NGS-pipe/wiki/Installation-&-Testing), I saw the the command lines for WGS …
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It would be nice to have a workflow option to 'delete intermediate files' after they have been used as input. There is currently a workflow option to 'Delete intermediate jobs if they are not used as …
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**Issue**
Class `GenomeCoverageReportStepPart` doesn't seem to be used for a while and also doesn't seem to work.
Source: `snappy_pipeline.workflows.ngs_mapping.GenomeCoverageReportStepPart` ([code]…