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nf-core · Nov 13, 2024 · 17b4a08 · 17b4a08
1 parent 7d15cb2
commit 17b4a08
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Showing 4 changed files with 3 additions and 35 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -8,6 +8,7 @@ references/rtgtools/genome.sdf/summary.txt
 references/rtgtools/genome.sdf/progress
 references/rtgtools/genome.sdf/format.log
 references/rtgtools/genome.sdf/mainIndex
+references/rtgtools/genome.sdf/done
 **/summary/tables/**/*.csv
 **/summary/datavzrd/versions.yml
 **/summary/datavzrd/**/index.html

diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
@@ -507,7 +507,6 @@
                 "small/test2/stats/bcftools/test2.bcftools.bcftools_stats.txt"
             ],
             [
-                "done:md5,1348e6a101bdcc2f2b1fb5d9a2d39fa2",
                 "nameIndex0:md5,720ad6dfad3d1ee07a3a2bc3ed953395",
                 "namedata0:md5,758c4a60948aed6c6a4c78323aa73ab3",
                 "namepointer0:md5,319f9f665b338f0e218677e036637e94",
@@ -551,6 +550,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-12T16:07:41.455769086"
+        "timestamp": "2024-11-13T08:41:21.414009313"
     }
 }
diff --git a/tests/liftover_hg38.nf.test b/tests/liftover_hg38.nf.test
@@ -17,37 +17,6 @@ nextflow_pipeline {
             }
         }
 
-        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_pipeline_software_mqc_versions.yml"),
-                    // All stable path name, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path
-                ).match() }
-            )
-        }
-    }
-    test("-stub") {
-
-        options "-stub"
-
-        when {
-            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}'])

diff --git a/tests/liftover_hg38.nf.test.snap b/tests/liftover_hg38.nf.test.snap
@@ -268,7 +268,6 @@
                 "small/test2/stats/bcftools/test2.bcftools.bcftools_stats.txt"
             ],
             [
-                "done:md5,095c6e81d56a0e3fe969e635ed49ff3b",
                 "nameIndex0:md5,720ad6dfad3d1ee07a3a2bc3ed953395",
                 "namedata0:md5,758c4a60948aed6c6a4c78323aa73ab3",
                 "namepointer0:md5,319f9f665b338f0e218677e036637e94",
@@ -313,7 +312,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-12T15:46:02.878306442"
+        "timestamp": "2024-11-13T09:00:38.410760165"
     },
     "-stub": {
         "content": [