From 16e978fc923c535489efd4d69b644858c4cfd29c Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:16:08 +0000 Subject: [PATCH 1/8] add illumina config to tests --- conf/test.config | 4 ++++ conf/test_index.config | 4 ++++ conf/test_no_genome.config | 4 ++++ conf/test_umi.config | 4 ++++ 4 files changed, 16 insertions(+) diff --git a/conf/test.config b/conf/test.config index 65137212..558e41b2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,3 +31,7 @@ params { cleanup = true //Otherwise tests dont run through properly. } + +// Include illumina config to run test without additional profiles + +includeConfig 'protocol_illumina.config' diff --git a/conf/test_index.config b/conf/test_index.config index 237251af..8a5a6532 100644 --- a/conf/test_index.config +++ b/conf/test_index.config @@ -32,3 +32,7 @@ params { cleanup = true //Otherwise tests dont run through properly. } + +// Include illumina config to run test without additional profiles + +includeConfig 'protocol_illumina.config' diff --git a/conf/test_no_genome.config b/conf/test_no_genome.config index cbc496ff..c918cd80 100644 --- a/conf/test_no_genome.config +++ b/conf/test_no_genome.config @@ -28,3 +28,7 @@ params { skip_mirdeep = true } + +// Include illumina config to run test without additional profiles + +includeConfig 'protocol_illumina.config' diff --git a/conf/test_umi.config b/conf/test_umi.config index cd359a6f..597409f2 100644 --- a/conf/test_umi.config +++ b/conf/test_umi.config @@ -33,3 +33,7 @@ params { umitools_bc_pattern = '.+(?PAACTGTAGGCACCATCAAT){s<=2}(?P.{12})(?P.*)' save_umi_intermeds = true } + +// Include illumina config to run test without additional profiles + +includeConfig 'protocol_illumina.config' From 037ef193fa062ce670b2f0a9d157e86bda05a018 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:16:24 +0000 Subject: [PATCH 2/8] add protocol clarification to docs --- README.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3db1a5b9..48134acf 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,15 @@ You can find numerous talks on the nf-core events page from various topics inclu > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. -First, prepare a samplesheet with your input data that looks as follows: +You can test the pipeline as follows: + +```bash +nextflow run nf-core/smrnaseq \ + -profile test \ + --outdir +``` + +In order to use the pipeline with your own data, first prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: @@ -107,6 +115,9 @@ nextflow run nf-core/smrnaseq \ --outdir ``` +> [!IMPORTANT] +> Remember to add a protocol as an additional profile (such as `illumina`, `nexttflex`, `qiaseq` or `custom`) when running with your own data. Default is `custom`. See [usage documentation](https://nf-co.re/smrnaseq/usage) for more details about these profiles. + > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). From 78b6c648ce701b6170f4b93f18d5cc2e2962e360 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:41:55 +0000 Subject: [PATCH 3/8] remove illumina profile from tests --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3463d872..997e6ef3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,10 +27,10 @@ jobs: - "23.04.0" - "latest-everything" profile: - - "test,illumina" - - "test_no_genome,illumina" - - "test_umi,illumina" - - "test_index,illumina" + - "test" + - "test_no_genome" + - "test_umi" + - "test_index" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 From 8a73eae15bf3ffe3e61a145668589d137931bfcb Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:42:14 +0000 Subject: [PATCH 4/8] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d5ffb78f..d16fb40f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel - [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue - [[#351]](https://github.com/nf-core/smrnaseq/issues/351) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/pull/364) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols +- [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix default tests so that they do not require additional profiles. ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch From 4a78a74b9f70d7ff89216f332c69f6b459f934d1 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 14 Aug 2024 16:14:09 +0000 Subject: [PATCH 5/8] revert changes in test_index --- .github/workflows/ci.yml | 2 +- conf/test_index.config | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 997e6ef3..309721f9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,7 +30,7 @@ jobs: - "test" - "test_no_genome" - "test_umi" - - "test_index" + - "test_index,illumina" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 diff --git a/conf/test_index.config b/conf/test_index.config index 8a5a6532..ef3dd250 100644 --- a/conf/test_index.config +++ b/conf/test_index.config @@ -33,6 +33,3 @@ params { cleanup = true //Otherwise tests dont run through properly. } -// Include illumina config to run test without additional profiles - -includeConfig 'protocol_illumina.config' From ba04df3e11260dab62a92076660666c72862bf33 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 16 Aug 2024 20:14:57 +0000 Subject: [PATCH 6/8] change fail-fast strategy to false and remove illumina profile from test --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 309721f9..dcbd4ff0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,6 +22,7 @@ jobs: if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}" runs-on: ubuntu-latest strategy: + fail-fast: false matrix: NXF_VER: - "23.04.0" @@ -30,7 +31,7 @@ jobs: - "test" - "test_no_genome" - "test_umi" - - "test_index,illumina" + - "test_index" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 From baa58de4cc99ad19945f5fe6621edad1a7305560 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 16 Aug 2024 20:18:55 +0000 Subject: [PATCH 7/8] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3770ed3d..32319e5c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel - [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue - [[#351]](https://github.com/nf-core/smrnaseq/issues/351) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/pull/364) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols -- [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix default tests so that they do not require additional profiles. +- [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix [default tests](https://github.com/nf-core/smrnaseq/issues/375) so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false. - [[#371]](https://github.com/nf-core/smrnaseq/issues/371) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/pull/372) - Updated default protocol value to "custom". ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch From ba48e8104857783ec3820e8e24aad9ccb7e4ee6c Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 16 Aug 2024 20:36:35 +0000 Subject: [PATCH 8/8] add llumina protocol to test index --- conf/test_index.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/test_index.config b/conf/test_index.config index ef3dd250..8a5a6532 100644 --- a/conf/test_index.config +++ b/conf/test_index.config @@ -33,3 +33,6 @@ params { cleanup = true //Otherwise tests dont run through properly. } +// Include illumina config to run test without additional profiles + +includeConfig 'protocol_illumina.config'