Merge remote-tracking branch 'origin/dev' into multiple-seqfu-reports

Author: Aratz

.github/workflows/awsfulltest.yml

@@ -45,9 +45,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

CHANGELOG.md

@@ -19,10 +19,13 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+- [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
+- [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 
 ### `Fixed`
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
+- [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 
 ### `Dependencies`
 

conf/test_full.config

@@ -10,14 +10,13 @@
 ----------------------------------------------------------------------------------------
 */
 
+
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

docs/images/nfcore-seqinspector-logo-hex-dark.png

@@ -229,27 +229,27 @@ def genomeExistsError() {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
-            "Tools used in the workflow included:",
-            "FastQC (Andrews 2010),",
-            "MultiQC (Ewels et al. 2016)",
-            "."
-        ].join(' ').trim()
+        "Tools used in the workflow included:",
+        "FastQC (Andrews 2010),",
+        "MultiQC (Ewels et al. 2016),",
+        "FastQ Screen (Wingett & Andrews 2018)",
+        params.sample_size > 0 ? "Seqtk (Li 2021)," : "",
+        "SeqFu (Telatin et al. 2021),",
+        "."
+    ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-        ].join(' ').trim()
+        "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.</li>",
+        "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>",
+        "<li>Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
+        params.sample_size > 0 ? "<li>Li, H. SeqTk. Available online: https://github.com/lh3/seqtk (accessed on 6 May 2021)</li>" : "",
+        "<li>Telatin, A.; Fariselli, P.; Birolo, G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059</li>"
+    ].join(' ').trim()
 
     return reference_text
 }
@@ -275,13 +275,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
-    meta["tool_citations"] = ""
-    meta["tool_bibliography"] = ""
-
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    // meta["tool_bibliography"] = toolBibliographyText()
-
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
     def methods_text = mqc_methods_yaml.text
 

docs/images/nfcore-seqinspector-logo-hex-dark.svg

@@ -0,0 +1,43 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on MiSeq data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("MiSeq data test") {
+
+        when {
+            config "./MiSeq_PairedEnd.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}

docs/images/nfcore-seqinspector-logo-hex-light.png

@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
+}