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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
Hapibd
## PR checklist Closes #XXX - [ ] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be...
## PR checklist Adding module wrapper for https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. See also https://nfcore.slack.com/archives/CJRH30T6V/p1665413183508719. Apologies for the long name, didn't quite think that through at the time I wrote this tool! Closes https://github.com/nf-core/modules/issues/2316...
### Have you checked the docs? - [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug There's no outputs caught because both bigWig and the...
Adding a new module for nanomonsv/parse. This is an SV caller for tumour/normal data from ONT sequencing. I have opened a PR for new test data https://github.com/nf-core/test-datasets/pull/664 Tests are passing...
Add the `parse` command from `nanomonsv`. I will also add the `get` command and other downstream commands after. ### Is there an existing module for this? - [X] I have...
I propose that we rename the `bam_dedup_stats_samtools_umitools` subworkflow to be just `bam_dedup_umitools`. [Various](https://github.com/nf-core/modules/blob/a52cd7df53f3e88895362f2c8fd43cfe00fbf1a3/subworkflows/nf-core/fastq_align_bowtie2/main.nf#L6) [other](https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/bam_markduplicates_picard/main.nf) [subworkflows](https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/fastq_align_hisat2/main.nf) generate stats using `samtools`, without mentioning it in the name of the subworkflow. I think...
Adds a module for creation of Shiny apps like [this](https://pinin4fjords.shinyapps.io/shinyngs_example/) with [shinyngs](https://github.com/pinin4fjords/shinyngs) via a CLI script. Not all features are yet available via the CLI, but I'm working on it....
Motivated by: https://aws.amazon.com/blogs/hpc/biocontainers-are-now-available-in-amazon-ecr-public-gallery/ They don't have mulled images being pushed yet however, but this should support other urls as well so it's a nice change.
### 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...
## PR checklist Closes #XXX - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...
