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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
## PR checklist Fixed extraction of KMERCOV, printf worked only for floating point numbers. Awk works both for floats and scientific notation. Also updated the container version (commit hash remains...
## PR checklist Closes #XXX - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...
When using MarkDuplicates on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be...
Removing the hardcoded output name and pointing to prefix instead ## PR checklist Closes #XXX - [X] This comment contains a description of changes (with reason). - [] If you've...
Still waiting for bioconda to upload the Biocontainer image of the core package (priorcons) priorcons: integrate_consensus module – generates high-quality viral consensus sequences by integrating a mapping consensus with ABACAS...
sorry this feels very draft status. move it into a another PR before merging this one _Originally posted by @mashehu in https://github.com/nf-core/modules/pull/6286#discussion_r1846901512_ ```yml # get-number-of-shards: # runs-on: ubuntu-latest # outputs:...
### 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 your feature request related to a problem? Please describe As of cellranger 10.0.0, VDJ analysis can be run reference free. - https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-multi-config-csv-opts#vdj - [Release notes](https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes#:~:text=Running%20V(D)J%20analysis%20in%20reference%2Dfree%20(i.e.%2C%20denovo)%20mode%20is%20now%20supported%20in%20cellranger%20multi.%20See%20the%20%5Bvdj%5D%20section%20of%20the%20Multi%20Config%20CSV%20page%20for%20further%20instructions.) This functionality should...
### 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 subworkflow for this? - [x] I have searched for the existing subworkflow ### Is there an open PR for this? - [x] I have searched...
