Alyssa Briggs

new module: trimmomatic

4

### 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...

Organize into subworkflows

1

Closes #58

### Description of feature - Currently supported on the [single-end branch](https://github.com/nf-core/viralintegration/tree/single-end) - Make second fastq input to `polyA_stripper` optional

### Description of feature - [x] HOST - [x] PLUS - [x] INSERTION_SITES - [x] VALIDATE - [x] CHIMERIC_READS

Update test data for nf-test/summary_report

2

### Description of feature https://github.com/nf-core/viralintegration/blob/summaryreport/tests/modules/summary_report/main.nf.test https://github.com/nf-core/test-datasets/tree/viralintegration/testdata/summary_report Use inputs from updated runs with full reference - [x] Nextflow full GRCh38 - [ ] CTAT/Cromwell full GRCh38