test: Add test assets#12
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### Added - `NEXTFLOW_RUN` local module based on based on [`mahesh-panchal/nf-cascade`](https://github.com/mahesh-panchal/nf-cascade).
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
### Added - `NFCORE_ONCOANALYSER` module using `NEXTFLOW_RUN` to main workflow. - Input parameters for running `oncoanalyser`: - `oncoanalyser_config` - `oncoanalyser_nextflow_opts` - `oncoanalyser_params_file` - `oncoanalyser_samplesheet` ### Changed - Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to nf-core/oncoanalyser#299. - Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. - Changed default test to not capture `pipeline_info` files for all pipelines.
…#6) ### Changed - Update test comment related to `clean_oncorefiner_params_file_content`.
…nalysis (#7) ### Fixed - `CREATE_ONCOREFINER_PARAMS_FILE` to: - add support for tumor only analysis. - fix bug in `bam/bai_tumor` file path.
…yser` (#8) Due to bug nf-core/oncoanalyser#301, purple output `tbi` are not produced by `oncoanalyser` when run in stub. These files are expected by `oncorefiner` which would lead the tests to fail. I have created a forked version https://github.com/Clinical-Genomics/oncoanalyser with branch `2.2.0-with-purple-tbi-fix` that includes a fix for this bug. Version `2.2.0` was the one used for test runs on hasta, so this PR also changes the version used to match this. When `nf-core/oncoanalyser` is patched, we can revert these changes to run the updated official release of the pipeline - see Clinical-Genomics/MTP-oncoflow#102. ### Changed - `NFCORE_ONCOANALYSER` to run forked fixed version `Clinical-Genomics/oncoanalyser `. - test config to run the above with revision `2.2.0-with-purple-tbi-fix`.
### Added - `NFCORE_ONCOREFINER` module using `NEXTFLOW_RUN` to `ONCOFLOW` workflow. - Input parameters for running `oncorefiner`: - `oncorefiner_config` - `oncorefiner_nextflow_opts` ### Changed - Updated `.nftignore` to ignore `vep` output files from `oncorefiner` - see https://github.com/Clinical-Genomics/oncorefiner/blob/f3b47fd369738465684ebaf62f04c44989d0cde6/tests/.nftignore#L12.
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