Update test files

nf-core · Aug 27, 2024 · b5d6812 · b5d6812
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,12 +31,9 @@ jobs:
           - "latest-everything"
         profile:
           - "test"
-          - "test_no_genome"
           - "test_umi"
-          - "test_index"
           - "test_technical_repeats"
           - "test_mirgenedb"
-          - "test_skipfastp"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,22 +5,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.4.0dev - 2024-XX-XX - X
 
-- [[#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.
+- [[#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.
 - [[#361]](https://github.com/nf-core/smrnaseq/pull/361) - Fix [[#332]](https://github.com/nf-core/smrnaseq/issues/332) - Fix documentation to use only single-end.
 - [[#364]](https://github.com/nf-core/smrnaseq/pull/364) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/issues/351) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols.
 - [[#372]](https://github.com/nf-core/smrnaseq/pull/372) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/issues/371) - Updated default protocol value to "custom".
 - [[#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.
 - [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test [technical repeats](https://github.com/nf-core/smrnaseq/issues/212) - Test merging of technical repeats.
 - [[#377]](https://github.com/nf-core/smrnaseq/pull/377) - Fix [Linting](https://github.com/nf-core/smrnaseq/issues/369) - Fixed linting warnings and updated modules & subworkflows.
-- [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>). Make `MIRTRACE` process conditional. Add mirgenedb test.
+- [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>) - Make `MIRTRACE` process conditional. Add mirgenedb test.
 - [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts.
 - [[#381]](https://github.com/nf-core/smrnaseq/pull/381) - Update [Convert tests to nf-tests](https://github.com/nf-core/smrnaseq/issues/379) - CI tests to nf-tests.
 - [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174) - Add nf-tests for local modules using custom R scripts.
 - [[#383]](https://github.com/nf-core/smrnaseq/pull/383) - Fix [parameter `--skip_fastp` throws an error](https://github.com/nf-core/smrnaseq/issues/263) - Fix parameter --skip_fastp.
 - [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360) - Fix filter stats module and add filter contaminants test profile.
-- [[#387]](https://github.com/nf-core/smrnaseq/pull/387) - Add nf-test to local module `blat_mirna` and fixes [contaminant filter failure because the Docker image for BLAT cannot be pulled](https://github.com/nf-core/smrnaseq/issues/354). Adds a small test profile to test contaminant filter results.
-- [[#391]](https://github.com/nf-core/smrnaseq/pull/391) - Change `.bai` index for `.csi` index in `samtools_index` to fix [error because of large chromosomes](https://github.com/nf-core/smrnaseq/issues/132).
+- [[#387]](https://github.com/nf-core/smrnaseq/pull/387) - Add [contaminant filter failure because the Docker image for BLAT cannot be pulled](https://github.com/nf-core/smrnaseq/issues/354) - Add nf-test to local module `blat_mirna` and fixes . Adds a small test profile to test contaminant filter results.
+- [[#391]](https://github.com/nf-core/smrnaseq/pull/391) - Fix [error because of large chromosomes](https://github.com/nf-core/smrnaseq/issues/132) - Change `.bai` index for `.csi` index in `samtools_index` to fix .
+- [[#392]](https://github.com/nf-core/smrnaseq/pull/392) - Update [Reduce tests](https://github.com/orgs/nf-core/projects/74/views/7?pane=issue&itemId=76437974) - Combine and optimize tests, and reduce samplesheets sizes.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/conf/test.config b/conf/test.config
@@ -23,13 +23,13 @@ params {
 
     input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
     fasta            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
+    bowtie_index     = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/bowtie_index.tar.gz'
 
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
     save_merged              = false
     save_aligned_mirna_quant = false
 
-    cleanup                  = true //Otherwise tests dont run through properly.
 }
 
 // Include illumina config to run test without additional profiles

diff --git a/conf/test_index.config b/conf/test_index.config
diff --git a/conf/test_mirgenedb.config b/conf/test_mirgenedb.config
@@ -34,7 +34,6 @@ params {
     save_merged              = false
     save_aligned_mirna_quant = false
 
-    cleanup                  = true //Otherwise tests dont run through properly.
 }
 
 // Include illumina config to run test without additional profiles

diff --git a/conf/test_no_genome.config b/conf/test_no_genome.config
diff --git a/conf/test_skipfastp.config b/conf/test_skipfastp.config
diff --git a/conf/test_technical_repeats.config b/conf/test_technical_repeats.config
@@ -9,6 +9,7 @@
 
 ----------------------------------------------------------------------------------------
 */
+// Tests covers techincal_repeats, skip_fastp and running without genome.
 
 params {
     config_profile_name        = 'Test technical repeats profile'
@@ -22,16 +23,18 @@ params {
     // 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
+    skip_fastp               = true
     save_merged              = false
     save_aligned_mirna_quant = false
 
     skip_fastqc                 = true
     skip_multiqc                = true
 
-
-    cleanup                  = true //Otherwise tests dont run through properly.
 }
+
+// Include illumina config to run test without additional profiles
+
+includeConfig 'protocol_illumina.config'
diff --git a/nextflow.config b/nextflow.config
@@ -141,7 +141,6 @@ profiles {
     debug {
         dumpHashes              = true
         process.beforeScript    = 'echo $HOSTNAME'
-        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
@@ -242,14 +241,11 @@ profiles {
 
     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_full_filter_contamination { includeConfig 'conf/test_full_filter_contamination.config' }
-    test_index                     { includeConfig 'conf/test_index.config' }
     test_technical_repeats         { includeConfig 'conf/test_technical_repeats.config' }
     test_mirgenedb                 { includeConfig 'conf/test_mirgenedb.config' }
     test_contamination             { includeConfig 'conf/test_contamination.config' }
-    test_skipfastp                 { includeConfig 'conf/test_skipfastp.config' }
 
 
     //Protocol specific profiles