Merge branch 'dev' into nf_tests_blat

.github/workflows/ci.yml

@@ -10,6 +10,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
+  NFTEST_VER: "0.9.0"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -47,6 +49,22 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: nf-test test tests/${{ matrix.profile }}.nf.test --profile +docker --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 execution_trace*
+.nf-test*

CHANGELOG.md

@@ -5,19 +5,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.4.0dev - 2024-XX-XX - X
 
-- [[#332]](https://github.com/nf-core/smrnaseq/issues/332) by [[#361]](https://github.com/nf-core/smrnaseq/pull/361) - Fix documentation to use only single-end
-- [[#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.
-- [[#369]](https://github.com/nf-core/smrnaseq/issues/369) - Fix [Linting](https://github.com/nf-core/smrnaseq/pull/377) - Fixed linting warnings and updated modules & subworkflows.
+- [[#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.
-- [[#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".
-- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts: [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187).
+- [[#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.
-- [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212).
-- [[#383]](https://github.com/nf-core/smrnaseq/pull/383) - Fixes [parameter `--skip_fastp` throws an error](https://github.com/nf-core/smrnaseq/issues/263).
-- [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add nf-tests for local modules using custom R scripts: [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174).
-- [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix filter stats module and add filter contaminants test profile: [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360).
+- [[#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.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

nextflow.config

@@ -21,8 +21,8 @@ params {
     igenomes_base               = 's3://ngi-igenomes/igenomes'
     igenomes_ignore             = false
     mirna_gtf                   = null
-    mature                      = "https://mirbase.org/download/mature.fa"
-    hairpin                     = "https://mirbase.org/download/hairpin.fa"
+    mature                      = "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa"
+    hairpin                     = "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa"
     mirgenedb                   = false
     mirgenedb_mature            = null
     mirgenedb_hairpin           = null

nextflow_schema.json

@@ -154,7 +154,7 @@
                     "description": "Path to FASTA file with mature miRNAs.",
                     "fa_icon": "fas fa-wheelchair",
                     "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.",
-                    "default": "https://mirbase.org/download/mature.fa"
+                    "default": "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa"
                 },
                 "mirgenedb_mature": {
                     "type": "string",
@@ -166,7 +166,7 @@
                     "description": "Path to FASTA file with miRNAs precursors.",
                     "fa_icon": "fab fa-cuttlefish",
                     "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.",
-                    "default": "https://mirbase.org/download/hairpin.fa"
+                    "default": "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa"
                 },
                 "mirgenedb_hairpin": {
                     "type": "string",

tests/lib/UTILS.groovy

@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}