Carson J Miller

New module: cobra-meta

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

Added ability to auto-create samplesheet for nf-core/phageannotator

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

Adding pipeline nf-tests to nf-core/mag

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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,...

### Description of feature Expand documentation to include when/why to use nf-core/mag, and potential downstream analyses that can be utilize nf-core/mag outputs. ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/mag/issues/589 -...

Add coverm/contig and coverm/genome as options for calculating read alignment metrics

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### Description of feature Add CoverM to calculate read alignment metrics for contig/bin alignments ```[tasklist] ### Tasks - [ ] Add coverm/contig to nf-core/modules - [ ] Add coverm/genome to...

pharokka (https://github.com/gbouras13/pharokka) is a tool used to functionally annotate phage sequences. It is similar to its bacterial counterparts (Prokka and Bakta). ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/modules/issues/4619 - [...

Generate samplesheet for nf-core/mag

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### Description of feature Add option to automatically generate a samplesheet than can be input into nf-core/mag