feat: Add shared config logic

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`
 

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,

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"}
+    }
+}

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(),
     )