Merge remote-tracking branch 'origin/dev' into purecn-support

nf-core · Oct 29, 2024 · dfc783e · dfc783e
2 parents d456dc2 + 1ba8cee
commit dfc783e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          # - "latest-everything"
+          - "latest-everything"
         filter: ["workflow", "function", "pipeline"]
         # filter: ["process", "workflow", "function", "pipeline"]
         profile: ["conda", "docker", "singularity"]

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1686](https://github.com/nf-core/sarek/pull/1686) - Template update for nf-core/tools v3.0.2
 - [1692](https://github.com/nf-core/sarek/pull/1692) - Update ensemblvep
 - [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules
+- [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
+- [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
 
 ### Fixed
 
@@ -34,10 +36,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1693](https://github.com/nf-core/sarek/pull/1693) - Fixes flowcell retrieval during samplesheet parsing
 - [1694](https://github.com/nf-core/sarek/pull/1694) - Fix manifest DOI display on CLI
 - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json
+- [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
 
 ### Removed
 
 - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
+- [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
 
 ### Dependencies
 

diff --git a/conf/test.config b/conf/test.config
@@ -22,13 +22,13 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Base directory for nf-core/modules test data
-    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
 
     // Input data
     input = "${projectDir}/tests/csv/3.0/fastq_single.csv"
 
     // small genome on igenomes
-    igenomes_base   = 's3://ngi-igenomes/testdata/nf-core/modules'
+    igenomes_base   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
     genome          = 'testdata.nf-core.sarek'
 
     // Small reference genome

diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
diff --git a/docs/output.md b/docs/output.md
@@ -554,7 +554,7 @@ In Sentieon's package DNAseq, joint germline variant calling is done by first ru
 For further downstream analysis, take a look [here](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#interpreting-the-germline-multi-sample-variants-vcf).
 
 <details markdown="1">
-<summary>Output files for all single samples (normal or tumor-only)</summary>
+<summary>Output files for single samples (normal)</summary>
 
 **Output directory: `{outdir}/variantcalling/strelka/<sample>/`**
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -559,7 +559,7 @@ Some of the currently, available test profiles:
 | no_intervals    | `nextflow run main.nf -profile test_cache,no_intervals,docker`                        |
 | targeted        | `nextflow run main.nf -profile test_cache,targeted,docker`                            |
 | tools_germline  | `nextflow run main.nf -profile test_cache,tools_germline,docker --tools strelka`      |
-| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools strelka`     |
+| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools mutect2`     |
 | tools_somatic   | `nextflow run main.nf -profile test_cache,tools_somatic,docker --tools strelka`       |
 | trimming        | `nextflow run main.nf -profile test_cache,trim_fastq,docker`                          |
 | umi             | `nextflow run main.nf -profile test_cache,umi,docker`                                 |
@@ -583,7 +583,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |    -    |   x   |    x    |
 | [lofreq](https://github.com/CSB5/lofreq)                                                                |  x  |  x  |   x    |    -    |   x   |    -    |
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
-| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
+| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   -   |    x    |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
 | [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |    -    |   -   |    x    |