SusiJo

Fix bcftools/stats module

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## PR checklist This PR fixes the module bcftools/stats and enables to use a regions (with index tbi files) or targets file (no index tbi file required) and adjusts the...

INFO/DP field not reported

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Hi there, We are using strelka for one of our pipelines and were wondering if it is possible to output the INFO/DP field in addition to the FORMAT/DP field. We...

Improve documentation: Troubleshooting

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### Description of feature Suggestion: Please add a troubleshooting section with common error messages that helps users to quickly understand what they're missing to get the pipeline running. I suggest...

Database annotations for Cucumis sativus

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**Describe the issue** For the organism _Cucumis sativus_ there are three database entries for different snpEff versions. However, it is not clear which genomes these entries refer to. Is there...

## PR checklist Fixes the ggsave error when many genes are DE. With many genes being DE, one might need to adapt resource requirements. Therefore, usage docs were updated to...

## PR checklist Only takes effect if a `gtf` file is provided as input and if the field `gene_biotype` is available in the attributes of the `gtf` file. - [x]...

Put gprofiler in tabs

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## PR checklist Closes #269. - [x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be...

### Description of feature Make sure that pathway analysis is run with a lot of DE genes and/or contrasts to analyze, consider parallelizing this step as it is currently simply...

### Description of feature background table for gprofiler is now written to the results, can be used manually in gprofiler, still text in html report needs to be adapted

### Description of feature Avoid duplicates gene names for heatmaps of enriched pathways.