Optitype wrapper (snakemake#128)

* Wrapper for razers3

* Optitype wrapper

* cleanup

* cleanup

* cleanup

* reformatted

Co-authored-by: jafors <[email protected]>

Updated wrapper for pTrimmer v1.3.2 (snakemake#115)

* Updated wrapper for pTrimmer v1.3.2

* Formatting

* Removed variable

* Import io

* Replace os by nthpath

* Fix stripping basename

* Changed parameter

* Changed parameter

* Changed parameter

* Fixed string-format

* Minor fix

fix gdc api token reading (snakemake#108)

* fix GDC API wrapper auth token parsing

* ran black code formatting

* use token via os.environ variable

* code formatting

always run vep in --offline mode

do not check for updates when downloading VEP cache

add curl dependency

Bedtools multiple file merging (snakemake#90)

* Added multifile merge

* Authorship

* Update test

* Removed formatting

* Fixed variables

* Error handling

* fmt

Simplified and more robust download of variation data (snakemake#104)

* try: simplified variation download, restricted on latest releases.

* grch37-test

* fixes

* fmt

* comment on minimum release

add gdc-client download wrapper (snakemake#98)

* initial commit for gdc-client wrapper

* gdc-client download: add test, add params.extra, add threads spec

* applied `black` code formatting

* gdc-client: introduce file moving to enable more freedom with file names

* gdc-client: adjust example rules to demonstrate freedom with file names

* applied `black` code formatting (including scripts and other wrappers)

* lots of debugging of gdc-client download wrapper

Merge branch 'master' of ssh://github.com/snakemake/snakemake-wrappers