Merlin Szymanski

broken report-file in singularity

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### Problem and Responsible Code Hi There is a problem in the way the report-file is created \ More specific: the way the **CL: statement** in the header is created...

DSL2: Metagenomics: Allow Skip-pairmerging before running metagenomics

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## Problem In dsl2/eager3 we currently dont allow the combination ```--run_metagenomics --preprocessing_skippairmerging``` because we are not handling paired reads in the metagenomics subworkflow ## ToDo One needs 1. Overhaul the...

## Problem We currently use the test-profiles for the metagenomics profilers just as a _technical_ test, that the pipeline runs smootly. But the output is always empty, because the current...

WIP: Nf test conversion: shortDNA

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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,...

We have both the `bamfiltering_genomicbamfilterflag` and the `bamfiltering_retainunmappedgenomicbam` flags. If I remember right, the idea at the beginning was to make the flag generic and restrain from named flags (e.g....

DSL2 - Host-removal keeps adapters in [DISCUSSION?]

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### Status Quo Host removal is a process to create fasta/fastq files (for ENA) without the host DNA. Currently, the fasta that go into the host removal process are the...