Merge pull request #177 from nf-core/homer-uniqmap

test(#57): Add uniqmap test

modules.json

@@ -125,7 +125,7 @@
                     },
                     "homer/findpeaks": {
                         "branch": "master",
-                        "git_sha": "b108745a1d59778e21577c217a963e17b8ba9bc2",
+                        "git_sha": "cac282aeb4099300e04b60167a3a12d8c96c4978",
                         "installed_by": ["homer_groseq"]
                     },
                     "homer/maketagdirectory": {
@@ -315,7 +315,7 @@
                     },
                     "homer_groseq": {
                         "branch": "master",
-                        "git_sha": "b108745a1d59778e21577c217a963e17b8ba9bc2",
+                        "git_sha": "cac282aeb4099300e04b60167a3a12d8c96c4978",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

workflows/tests/inputs/uniqmap/main.nf.test

@@ -0,0 +1,54 @@
+nextflow_pipeline {
+
+    name "HOMER Uniqmap"
+    script "../../../../main.nf"
+    tag "input"
+    tag "homer"
+
+    test("Should run with an zipped uniqmap") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                use_homer_uniqmap = true
+                homer_uniqmap = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/uniqmap.GRCh38_chr21.50nt.zip'
+                skip_grohmm = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                // Files should have -uniqmap <directory> in the header
+                { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
+                { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20].contains("-uniqmap") },
+                { assert path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
+                { assert path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[20].contains("-uniqmap") },
+                    // TODO Test for uniqmap unzip process
+                // { assert workflow.trace.tasks().find { it.process == "UNZIP" } },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                    path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18],
+                    path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20],
+                    path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[18],
+                    path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[20],
+                    path("$outputDir/transcript_identification/homer/cd4.bed"),
+                    path("$outputDir/transcript_identification/homer/jurkat.bed"),
+                    path("$outputDir/transcript_identification/homer/cd4-uniqmap.GRCh38_chr21.peaks.txt"),
+                    path("$outputDir/transcript_identification/homer/jurkat-uniqmap.GRCh38_chr21.peaks.txt"),
+                    path("$outputDir/transcript_identification/intersect/").list(),
+                    path("$outputDir/transcript_identification/filtered/").list(),
+                    // FIXME Not determinstic because of the order of files
+                    // Add to the other tests when fixed
+                    // path("$outputDir/quantification/").list(),
+                    path("$outputDir/multiqc/multiqc_report.html").exists(),
+                ).match("output_files")
+                },
+            )
+        }
+    }
+    // TODO Check for running with unzipped uniqmap
+}