Add nf-core CI

[samuell]

This PR adds GitHub Actions CI pipelines recommended and included in the nf-core template.

It also fixes some issues reported by an initial run with the nf-core lint tool.

• Add missing TEMPLATE branch (see here)

[samuell]

There are some syntax problems with some files, preventing the linting from completing:

prettier.................................................................Failed                                                                                                                             
         - hook id: prettier                                                                                                                                                                                         
         - exit code: 2                                                                                                                                                                                              
                                                                                                                                                                                                                     
         ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/assets/email_template.html                                                                                                                
         ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/.github/ISSUE_TEMPLATE/bug_report.yml                                                                                                     
         ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/.nf-core.yml                                                                                                                              
                                                                                                                                                                                                                     
          ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/assets/adaptivecard.json: SyntaxError: Unexpected token (57:47)                                                                          
            55 |                                 {                                                                                                                                                                   
            56 |                                     "type": "FactSet",                                                                                                                                              
          > 57 |                                     "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>                                                           
               |                                               ^                                                                                                                                                     
            58 |                                     ]                                                                                                                                                               
            59 |                                 }                                                                                                                                                                   
            60 |                             ]                                                                                                                                                                       
         ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/README.md                                                                                                                                 
                                                                                                                                                                                                                     
          ../../../../../../tmp/tmpezw_7axu/genomic-medicine-sweden-GMS_16S/assets/slackreport.json: SyntaxError: Unexpected token (15:18)                                                                           
            13 |                     "short": false                                                                                                                                                                  
            14 |                 }                                                                                                                                                                                   
          > 15 |                 <%                                                                                                                                                                                  
               |                  ^                                                                                                                                                                                  
            16 |                     if (!success) { %>                                                                                                                                                              
            17 |                     ,                                                                                                                                                                               
            18 |                     {       

[samuell]

As I think @sofstam mentioned, we should try to set up the process for syncing updates to the nf-core template, according to this guide. Seems to need some manual fixing to get it updated and "in sync".

[samuell]

This draft PR was accidentally closed. Opening a new one ...