diff --git a/CHANGELOG.md b/CHANGELOG.md index e214fe8..e6eb8ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added metadata parameters `case_id`, `sample_id_tumor`, `sample_id_normal`, `subject_id` and `sex`, necessary for creating the `oncorefiner` params file using the `CREATE_ONCOREFINER_PARAMS_FILE` local module. - [#10](https://github.com/Clinical-Genomics/oncoflow/pull/10) Added `getOncorefinerParamsList` function to produce the list of parameters necessary for `CREATE_ONCOREFINER_PARAMS_FILE`. - [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Added `CLINICAL_GENOMICS_ONCOREFINER` using the `NEXTFLOW_RUN` local module to run the `Clinical-Genomics/oncorefiner` pipeline in `ONCOFLOW` workflow. -- [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Added input parameters for running `Clinical-Genomics/oncorefiner`: `oncorefiner_config` and `oncorefiner_nextflow_opts`. +- [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Added input parameter for running `Clinical-Genomics/oncorefiner`: `oncorefiner_nextflow_opts`. ### `Changed` diff --git a/main.nf b/main.nf index 2f5e311..66cf7cb 100644 --- a/main.nf +++ b/main.nf @@ -28,13 +28,12 @@ workflow CLINICALGENOMICS_ONCOFLOW { take: val_case_id // string: [mandatory] Case ID - val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline + val_config // string: [optional] Config file for oncoanalyser pipeline val_oncoanalyser_create_stub_placeholders // bool: [mandatory] Create stub placeholders for oncoanalyser pipeline val_oncoanalyser_genome // string: [mandatory] Genome for oncoanalyser pipeline val_oncoanalyser_mode // string: [mandatory] Mode for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline val_outdir // string: [mandatory] The output directory where the results will be saved val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample @@ -49,13 +48,12 @@ workflow CLINICALGENOMICS_ONCOFLOW { // ONCOFLOW ( val_case_id, - val_oncoanalyser_config, + val_config, val_oncoanalyser_create_stub_placeholders, val_oncoanalyser_genome, val_oncoanalyser_mode, val_oncoanalyser_nextflow_opts, val_oncoanalyser_samplesheet, - val_oncorefiner_config, val_oncorefiner_nextflow_opts, val_outdir, val_sample_id_tumor, @@ -98,13 +96,12 @@ workflow { // CLINICALGENOMICS_ONCOFLOW ( params.case_id, - params.oncoanalyser_config, + workflow.configFiles[0], params.oncoanalyser_create_stub_placeholders, params.oncoanalyser_genome, params.oncoanalyser_mode, params.oncoanalyser_nextflow_opts, params.oncoanalyser_samplesheet, - params.oncorefiner_config, params.oncorefiner_nextflow_opts, params.outdir, params.sample_id_tumor, diff --git a/tests/nextflow.config b/tests/nextflow.config index 1a1ab93..9a61202 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,11 +4,15 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/oncoflow/' } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners + +process { + withName: '.*' { + ext.prefix = { "oncoflow_test"} + } +} diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 18317c7..97a5b38 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -21,13 +21,12 @@ workflow ONCOFLOW { take: val_case_id // string: [mandatory] Case ID - val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline + val_config // string: [optional] Config file for oncoanalyser pipeline val_oncoanalyser_create_stub_placeholders // bool: [mandatory] Create stub placeholders for oncoanalyser pipeline val_oncoanalyser_genome // string: [mandatory] Genome for oncoanalyser pipeline val_oncoanalyser_mode // string: [mandatory] Mode for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline val_outdir // string: [mandatory] The output directory where the results will be saved val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample @@ -54,7 +53,7 @@ workflow ONCOFLOW { val_oncoanalyser_nextflow_opts, CREATE_ONCOANALYSER_PARAMS_FILE.out.params_file, val_oncoanalyser_samplesheet, - val_oncoanalyser_config, + val_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) @@ -76,7 +75,7 @@ workflow ONCOFLOW { val_oncorefiner_nextflow_opts, CREATE_ONCOREFINER_PARAMS_FILE.out.params_file, '', - val_oncorefiner_config, + val_config, workflow.workDir.resolve('Clinical-Genomics/oncorefiner').toUriString(), )