Alyssa Briggs

Creating module for [trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) Using [cutadapt](https://github.com/nf-core/modules/blob/7a83ca30704e002bc4ba79d892ba364592c6db7f/modules/cutadapt/main.nf) as a reference module for a similar process.

[Script main.nf](https://github.com/alyssa-ab/modules/blob/trimmomatic/modules/trimmomatic/main.nf) [Test main.nf](https://github.com/alyssa-ab/modules/blob/trimmomatic/tests/modules/trimmomatic/main.nf)

Test fails [Command exit status: 1] .command.err output ```Command error: Usage: PE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] [-validatePairs] [-basein | ] [-baseout | ] ... or:...

Hi, just wanted to check a few things with you about the error. 1. Did you initially run your data through the pipeline and find that there were no results,...

For CTAT/Cromwell run, use Docker container (v1.4.0) which was updated with the latest release 4 months ago - Singularity version run initially was v1.01

Nextflow inputs added: https://github.com/nf-core/viralintegration/pull/38