Merge pull request #376 from atrigila/technical_repeats

Add test for technical repeats
nf-core · Aug 19, 2024 · 6e01548 · 6e01548
2 parents f69721e + f10ffa8
commit 6e01548
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -32,6 +32,7 @@ jobs:
           - "test_no_genome"
           - "test_umi"
           - "test_index"
+          - "test_technical_repeats"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#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".
+- [[#375](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212)
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/conf/test_technical_repeats.config b/conf/test_technical_repeats.config
@@ -0,0 +1,37 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/smrnaseq -profile test_technical_repeats,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test technical repeats profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+
+    input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats.csv'
+    fasta            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
+
+    mirtrace_species         = 'hsa'
+    skip_mirdeep             = true
+    save_merged              = false
+    save_aligned_mirna_quant = false
+
+    skip_fastqc                 = true
+    skip_multiqc                = true
+
+
+    cleanup                  = true //Otherwise tests dont run through properly.
+}
diff --git a/nextflow.config b/nextflow.config
@@ -238,11 +238,12 @@ profiles {
         executor.memory         = 60.GB
 
     }
-    test           { includeConfig 'conf/test.config' }
-    test_umi       { includeConfig 'conf/test_umi.config' }
-    test_no_genome { includeConfig 'conf/test_no_genome.config' }
-    test_full      { includeConfig 'conf/test_full.config' }
-    test_index     { includeConfig 'conf/test_index.config' }
+    test                        { includeConfig 'conf/test.config' }
+    test_umi                    { includeConfig 'conf/test_umi.config' }
+    test_no_genome              { includeConfig 'conf/test_no_genome.config' }
+    test_full                   { includeConfig 'conf/test_full.config' }
+    test_index                  { includeConfig 'conf/test_index.config' }
+    test_technical_repeats      { includeConfig 'conf/test_technical_repeats.config' }
 
     //Protocol specific profiles
     cats           { includeConfig 'conf/protocol_cats.config' }