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Added test_nothing nf-test and updated CI

3

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

CarsonJM

### Description of feature Release announcement: https://ecogenomics.github.io/GTDBTk/announcements.html#gtdb-tk-2-4-0-available Path to reference data: https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/

amizeranschi

### Description of feature This is a feature request to add an updated and well maintained version of prodigal called [Pyrodigal](https://github.com/althonos/pyrodigal). - It has exactly the same functionality as prodigal...

jasmezz

### Description of feature Allowing Prodigal to produce a gbk file instead of the gff would enable users to add annotations produced by `nf-core/mag` as input to `nf-core/funcscan`. Original discussion...

amizeranschi

CAT_DB process has harcoded CAT subdirectory names

1

### Description of the bug In the CAT_DB process, the subdirectories names are hardcoded (to `database` and `taxonomy`), which is problematic because the newer versions of the CAT database these...

maxibor

Post 3.2.0 release version bump

1

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

jfy133

Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs

3

Closes #687 and #686 This adds the local subworkflow (and other relevant code and docs) for generating samplesheets for the downstream pipelines funcscan and taxprofiler. ## PR checklist - [x]...

vagkaratzas

Running BUSCO with your own database

1

### Description of the bug Hi I tried to use BUSCO for the bin checking. Since our cluster does not allow to download things when inside a slurm job, I...

Thomieh73

Prokka: contig length too long - add option for `--compliant` mode

6

### Description of the bug I am running nf-core/mag 3.0.3 on a sample (ERR4303137) and it fails during the Prokka step. This looks like it might be a simple fix...

audy

--host_fasta_bowtie2index path taken for bowtie -S output file

2

### Description of the bug When I run nf-core/mag with the ``` --host_fasta_bowtie2index "/path/to/references/" ``` The bowtie log file gives me the following warning ``` Warning: Output file './references/reference_name' was...

MeriamOs