feat: add oncoanaliser+oncorefiner cascade - #1
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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.
### Added - `getOncorefinerParamsList` function to produce the list of parameters necessary for the oncorefiner params file. ### Changed - Generalised `CREATE_PARAMS_FILE` local modules to generate params files for any pipeline. - Call `CREATE_ONCOREFINER_PARAMS_FILE` using `CREATE_PARAMS_FILE` to `ONCOFLOW` workflow.
This PR uses the `CREATE_PARAMS_FILE` module to generate a params file for `oncoanalyser` so that `oncoflow` can receive only 1 params file and independently start all included pipelines. ### Added - `CREATE_ONCOANALYSER_PARAMS_FILE` using `CREATE_PARAMS_FILE` to `ONCOFLOW` workflow. - `getOncoanalyserParamsList` function to produce the list of parameters necessary for `CREATE_ONCOANALYSER_PARAMS_FILE`. - Added input parameters `oncoanalyser_create_stub_placeholders`, `oncoanalyser_genome` and `oncoanalyser_mode` necessary for creating the `oncoanalyser` params file using the `CREATE_ONCOANALYSER_PARAMS_FILE` local module. ### Changed - Removed `oncoanalyser_params_file` input parameter.
From https://github.com/mahesh-panchal/nf-cascade/wiki/Guided-Example-%E2%80%90-Nf%E2%80%90core-style-workflow: "Lastly, create a nextflow.config and add process.errorStrategy = 'finish'. Without this, if a pipeline errors, any concurrently running workflows will be killed immediately leaving a nextflow lock file in place preventing the workflow from resuming." ### Changed - Set `process.errorStrategy = 'finish'` for all processes.
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Closes https://github.com/Clinical-Genomics/MTP-oncoflow/issues/10.
Summary
Input:
oncoanalyserandoncorefinerparametersoncoanalyserandoncorefinerProcesses:
CREATE_ONCOANALYSER_PARAMS_FILENFCORE_ONCOANALYSER(running forked version Clinical-Genomics/oncoanalyser*)CREATE_ONCOREFINER_PARAMS_FILECLINICAL_GENOMICS_ONCOREFINERThe cascade handles the logic of creating the params files for
oncoanalyserandoncorefinerand propagate theoncoflowconfig file for all run pipelines.Default test runs all pipelines in stub mode:
Clinical-Genomics/oncoanalyserrevision2.2.0-with-purple-tbi-fixClinical-genomics/oncorefinerrevisiondevOutput:
Includes PRs:
NEXTFLOW_RUNlocal module #2NFCORE_ONCOANALYSERto main workflow #3CREATE_ONCOREFINER_PARAMS_FILElocal module #5add-create-oncorefiner-params-file#6CREATE_ONCOREFINER_PARAMS_FILEto add support for tumor only analysis #7NFCORE_ONCOANALYSERto run forked patched version ofoncoanalyser#8oncorefiner#4CREATE_PARAMS_FILElocal module #10CREATE_ONCOANALYSER_PARAMS_FILE#9process.errorStrategy#11Based on https://github.com/mahesh-panchal/nf-cascade/wiki/Guided-Example-%E2%80%90-Nf%E2%80%90core-style-workflow.
Added
NEXTFLOW_RUNlocal module based onmahesh-panchal/nf-cascade.NFCORE_ONCOANALYSERmodule usingNEXTFLOW_RUNtoONCOFLOWworkflow.oncoanalyser:oncoanalyser_configoncoanalyser_nextflow_optsoncoanalyser_params_fileoncoanalyser_samplesheetCREATE_ONCOREFINER_PARAMS_FILElocal module.case_idsample_id_tumorsample_id_normalsubject_idsexCREATE_ONCOREFINER_PARAMS_FILEmodule toONCOFLOWworkflow.Changed
.nftignoreto ignorepipeline_infoandmultiqcfiles for all pipelines..nftignoreto ignore gzipped output files fromoncoanalyserdue to Stub blocks for several modules that output gzipped files have incorrect syntax nf-core/oncoanalyser#299..nftignoreto ignore*.command.*output files fromoncoanalysersince several files include the run directory and platform information which changes for each run and therefore cannot be snapshot.pipeline_infofiles for all pipelines.Fixed
Removed