From 5aef85a2b6dd8773c1cbabde728bbb3fb89d1cb2 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 9 Jul 2026 17:09:37 +0200 Subject: [PATCH 1/6] Add shared config logic. --- main.nf | 9 +++------ tests/nextflow.config | 3 +++ workflows/oncoflow.nf | 7 +++---- 3 files changed, 9 insertions(+), 10 deletions(-) diff --git a/main.nf b/main.nf index e958f6e..21177f9 100644 --- a/main.nf +++ b/main.nf @@ -28,11 +28,10 @@ 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_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file 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 @@ -47,11 +46,10 @@ workflow CLINICALGENOMICS_ONCOFLOW { // ONCOFLOW ( val_case_id, - val_oncoanalyser_config, + val_config, val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, - val_oncorefiner_config, val_oncorefiner_nextflow_opts, val_sample_id_tumor, val_sample_id_normal, @@ -93,11 +91,10 @@ workflow { // CLINICALGENOMICS_ONCOFLOW ( params.case_id, - params.oncoanalyser_config, + workflow.configFiles[0], params.oncoanalyser_nextflow_opts, params.oncoanalyser_params_file, params.oncoanalyser_samplesheet, - params.oncorefiner_config, params.oncorefiner_nextflow_opts, params.sample_id_tumor, params.sample_id_normal, diff --git a/tests/nextflow.config b/tests/nextflow.config index 1a1ab93..4c782d4 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -12,3 +12,6 @@ params { } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners + + +//TODO diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index ac85ba0..037102f 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -18,11 +18,10 @@ 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_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file 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 @@ -39,7 +38,7 @@ workflow ONCOFLOW { val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, - val_oncoanalyser_config, + val_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) @@ -58,7 +57,7 @@ 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(), ) From f7f84ffe91a274541aa33ec742b33966a957beb1 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 10 Jul 2026 10:09:17 +0200 Subject: [PATCH 2/6] Restore tests/nextflow.config --- tests/nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 4c782d4..1a1ab93 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -12,6 +12,3 @@ params { } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners - - -//TODO From 9c58a6d3b890152be0f5c5f0aa7e5129bb7c6953 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 10 Jul 2026 10:10:13 +0200 Subject: [PATCH 3/6] Update changelog. --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cabfdf5..1e2fde9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,13 +11,13 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) Added `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline in `ONCOFLOW` workflow. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_config`, `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) and [#10](https://github.com/Clinical-Genomics/oncoflow/pull/10) Added `CREATE_PARAMS_FILE` local module. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) and [#10](https://github.com/Clinical-Genomics/oncoflow/pull/10) Added `CREATE_ONCOREFINER_PARAMS_FILE` using `CREATE_PARAMS_FILE` to `ONCOFLOW` workflow. - [#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` From 1ba52a162fb24785d3048c00954572f5a897e2b7 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 10 Jul 2026 10:13:49 +0200 Subject: [PATCH 4/6] Update changelog. --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1e2fde9..fc9120a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) 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. - [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed `NFCORE_ONCOANALYSER` to run forked fixed `Clinical-Genomics/oncoanalyser` instead, due to bug https://github.com/nf-core/oncoanalyser/issues/301. - [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed test config to run the above with revision `2.2.0-with-purple-tbi-fix` which includes the fix for https://github.com/nf-core/oncoanalyser/issues/301 and `nf-core/oncoanalyser` version 2.2.0 since this was the version used for previous test runs. +- [#11](https://github.com/Clinical-Genomics/oncoflow/pull/11) Set `process.errorStrategy = 'finish'` for all processes. ### `Fixed` From eeb1f3208e595741b3906335b8456277b7bd49bd Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 10 Jul 2026 10:14:41 +0200 Subject: [PATCH 5/6] Revert accidental change to changelog. --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc9120a..1e2fde9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,6 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) 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. - [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed `NFCORE_ONCOANALYSER` to run forked fixed `Clinical-Genomics/oncoanalyser` instead, due to bug https://github.com/nf-core/oncoanalyser/issues/301. - [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed test config to run the above with revision `2.2.0-with-purple-tbi-fix` which includes the fix for https://github.com/nf-core/oncoanalyser/issues/301 and `nf-core/oncoanalyser` version 2.2.0 since this was the version used for previous test runs. -- [#11](https://github.com/Clinical-Genomics/oncoflow/pull/11) Set `process.errorStrategy = 'finish'` for all processes. ### `Fixed` From 80680fe258603cac32d4319e95ac58f779fcfe98 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 10 Jul 2026 11:08:50 +0200 Subject: [PATCH 6/6] Add test settings to tests/nextflow.config. --- tests/nextflow.config | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) 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"} + } +}