update tests

nf-core · Oct 17, 2024 · a689e0f · a689e0f
1 parent 16df32b
commit a689e0f
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Showing 2 changed files with 4 additions and 11 deletions.
diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf
@@ -29,17 +29,18 @@ process SVDB_MERGE {
 
     if (sort_inputs && vcfs.collect().size() > 1) {
         if (priority) {
-            // If there are more than one input, make vcf-prioprity pairs
-            // pair them and sort on VCF name, so priority is also sorted the same
+            // make vcf-prioprity pairs and sort on VCF name, so priority is also sorted the same
             def pairs = vcfs.indices.collect { [vcfs[it], priority[it]] }
             pairs = pairs.sort { a, b -> a[0].name <=> b[0].name }
             vcfs = pairs.collect { it[0] }
             priority = pairs.collect { it[1] }
         } else {
+            // if there's no priority input just sort the vcfs by name
             vcfs = vcfs.sort { it.name }
         }
     }
 
+    // If there's only one input VCF the code above is not executed, and that VCF becomes the input
     input = vcfs
 
     def prio = ""

diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test
@@ -30,7 +30,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -61,7 +60,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -92,7 +90,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:tiddit") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -123,7 +120,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:tiddit") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -155,7 +151,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test2.vcf test.vcf") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test2\ttest") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -187,7 +182,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf test2.vcf") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test\ttest2") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -219,7 +213,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test2.vcf:tiddit test.vcf:cnvnator") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test2\ttest") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
@@ -230,7 +223,7 @@ nextflow_process {
     }
 
     test("2 samples, ['tiddit', 'cnvnator'], true") {
-        
+
         when {
             process {
                 """
@@ -251,7 +244,6 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:cnvnator test2.vcf:tiddit") }, // SVDB command line
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip[51].contains("test\ttest2") }, // #CHROM line
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,