Merge pull request #374 from atrigila/test_profile

Change profile configuration for CI tests
nf-core · Aug 19, 2024 · f69721e · f69721e
2 parents e343bbd + ba48e81
commit f69721e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,15 +22,16 @@ 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"
           - "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

diff --git 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](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

diff --git 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 <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 <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).

diff --git 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
@@ -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
@@ -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
@@ -33,3 +33,7 @@ params {
     umitools_bc_pattern = '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)'
     save_umi_intermeds = true
 }
+
+// Include illumina config to run test without additional profiles
+
+includeConfig 'protocol_illumina.config'