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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
Subworkflow to parallelize duplicate marking. Open for comments cfr https://nfcore.slack.com/archives/CGFUX04HZ/p1652439308069099 @FriederikeHanssen ```mermaid flowchart LR SPLIT_BAM[List of sorted bam chunks] --> BAMTOOLS_SPLIT -->|per chromosome| BAMMARKDUPLICATES2 --> SAMTOOLS_MERGE ``` ## PR checklist...
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
The latest version of Bioperl is causing some issues with Prokka. (See related issue: https://github.com/tseemann/prokka/issues/598) ``` Bio::SearchIO: hmmer3 cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module...
I think it would be good to have a module for Sentieon (https://bioconda.github.io/recipes/sentieon/README.html) LocusCollector (first step in marking duplicates). - [x] This module does not exist yet with the [`nf-core...
I think it would be good to have a module for Sentieon (https://bioconda.github.io/recipes/sentieon/README.html) Dedup (second step in marking duplicates). - [x] This module does not exist yet with the [`nf-core...
I think it would be good to have a module for [trycycler](https://bioconda.github.io/recipes/trycycler/README.html) - [x] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command - [x] There is...
maybe we can also have a section here about information about the module. I.e. website, conda package etc.. _Originally posted by @FriederikeHanssen in https://github.com/nf-core/modules/pull/1583#discussion_r861788396_
I'm assuming that since this option exists, there might be some case where we actually do not want index created. Don't want to push for that in https://github.com/nf-core/modules/pull/1584 so creating...
