Changelog

version 1.1.0

Update multiqc to version 1.10.
Update CutAdapt to version 3.4.
Update biowdl-input-converter to version 0.3.
Add the dockerImages to the output section.
Replace travis with github CI.
Update CutAdapt to version 3.0.0.
Remove metrics file from classification (which causes the summary report to be empty). DaehwanKimLab/centrifuge#83
Adapt the pipeline so it can also handle fasta files.

Update tasks and the input/output names.
Rename workflow outputs to shorter names.
Add meta {allowNestedInputs: true} to the workflows, to allow for the use of nested inputs.
Remove execute from the naming structure for calls of tasks and workflows.
Add centrifuge kreport to the pipeline.
Make the multiqc task suitable for use with a final_workflow_outputs_dir so it can be used on all of cromwell's supported backends.
Tasks were updated to contain the time_minutes runtime attribute and associated timeMinutes input, describing the maximum time the task will take to run.
Renamed workflow from pipeline to Classification.
Removed jenkinsfile from repo.
Update documentation with more specific example of sample sheet csv file.
Update cutadapt to 2.8.
Update multiqc to 1.8.
Update fastqc to 0.11.9.
Remove unused docker image.
Add cromwell test config.
Add krona plot.
Setup the centrifuge pipeline.