* Fix typo
* Add stub runs for testing input without matched normals
* Add missing -stub-run
* remove empty file checksum tests and change workflow names
* test controlfreec naming
* fix output file names
* fix output file names
* fix output file names
* fix conda and container path difference for R scripts
* update tar version to work with conda
* fix version number in docker
* try to fix path to script, pretty sure it won't work
* try new ways to set path with wildcard
* try which
* add which but with escape
* remove comment
* controlfreec significance
* move freec files to own subfolder
* Fix meta.yml naming
* Fix meta.yml naming
* Fix linting
* Forgot to refactor
* forgot more refactoring
* Too much refactoring on output paths
* Too little refactoring here
* update checksum
* style: Add prettier config files
* build: Add prettier vscode extension
* ci: Replace markdownlint and yamllint with prettier
* style: Run prettier
* style: Use indent of 2 for markdown as well
https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358
* style: Fix indent
* style: Let editorconfig take over tab widths
* style: yaml => yml
* ci: Run prettier once
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
* add drafty controlfreec
* get sofatware version
* use maps in map
* update paths to new and soon-to-be merged test files, add more input docu
* Stab at documenting args map
* Update syntax
* Bit more description
* Make the linter happy
* tests pass locally
* Add outputs & docu
* tests are failing locally now :/ but cpn file can also be added
* All tests passing, need to update test data again to add folder
* Clean up files
* Clean up files
* Clean up files
* Don't know how to get the test to run with the direcotry for now. they pass locally though
* Make linter happy
* Name process back
* Update to use tar folder
* fix the checksum
