Friederike Hanssen

**Is your feature request related to a problem? Please describe.** At the moment, there seems to be no concise guide on how to use nf-core/tools for custom pipelines and how...

#### Description Add module for nextflow (https://github.com/nextflow-io/nextflow). When a `.nf` file or a `nextflow.config` file is present, the version is printed. #### Screenshots (if appropriate): ![Screenshot 2022-12-13 at 22 43...

Allow existing GenomicsDb as input to incrementally update

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

Restart from step variantcalling fails on NGScheckmate

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### Description of the bug ``` ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (1)' Caused by: Not a valid path value: '../data/references/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed' ``` NGSCHeckmate should not even be running...

Restart from step variantcalling fails on haplotypecaller

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### Description of the bug q ### Command used and terminal output ```console nextflow run nf-core/sarek -r 3.4.2 -latest -profile docker --input data/markduplicates_no_table_local.csv --outdir ./test_single_sample --igenomes_base ../data/references --step variant_calling --tools...

### Description of feature Looking through the schema file recently I noticed that not all variables received the same love when it comes to adding a useful description or being...

### Description of the bug Running `nf-core create-params-file --show-hidden` for nf-core/sarek creates a yml file that still lists: ``` ## (1 hidden parameters are not shown) ``` etc. . The...

`modules update` with `patch` deletes files in `templates`

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### Description of the bug I customised the multiqc module to have a `templates` folder. I then applied `nf-core modules patch` which generates a `diff` file for the `main.nf` If...

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

**Describe the bug** The navigation for the subworkflows page, like the search and tiles vs list view is not responding. The same works on the modules page. **To Reproduce** Steps...