add bwameth run_qualimap test

nf-core · Dec 2, 2024 · 754065d · 754065d
1 parent d6917c3
commit 754065d
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Showing 4 changed files with 631 additions and 7 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -14,7 +14,7 @@ multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_sources.txt
 multiqc/{bismark,bismark_hisat,bwameth}/multiqc_report.html
 multiqc/{bismark,bismark_hisat,bwameth}/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg}
 pipeline_info/*.{html,json,txt,yml}
-qualimap/**/qualimapReport.html
+{bismark,bismark_hisat,bwameth}/qualimap/bamqc/*/qualimapReport.html
 qualimap/**/css/*
 qualimap/**/images_qualimapReport/*
 qualimap/**/raw_data_qualimapReport/*

diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap
@@ -556,7 +556,6 @@
                 "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31",
                 "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d",
                 "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d",
-                "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039",
                 "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4",
                 "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e",
                 "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25",
@@ -601,7 +600,6 @@
                 "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4",
                 "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef",
                 "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685",
-                "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d",
                 "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803",
                 "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2",
                 "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1",
@@ -643,7 +641,6 @@
                 "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956",
                 "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157",
                 "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19",
-                "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4",
                 "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2",
                 "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80",
                 "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8",
@@ -685,7 +682,6 @@
                 "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92",
                 "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de",
                 "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03",
-                "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973",
                 "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce",
                 "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301",
                 "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b",
@@ -752,6 +748,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T09:47:26.992492832"
+        "timestamp": "2024-12-02T12:34:53.964190449"
     }
-}
+}
diff --git a/tests/bwameth_run_qualimap.nf.test b/tests/bwameth_run_qualimap.nf.test
@@ -0,0 +1,42 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+    config "./nextflow.config"
+    tag "cpu"
+
+    test("Params: bwameth | run_qualimap") {
+        when {
+            params {
+                aligner       = "bwameth"
+                outdir       = "$outputDir"
+                run_qualimap = true
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+}