* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
* fix multiqc process
* fix multiqc tests
* move multiqc test input data into tests/data/fastqc/ folder
Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation
* add multiqc github workflow
* remove unused file
* generalize multiqc input data
User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report
* update meta information
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
