Merge branch 'master' into nf-test_phispy

* master: Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. (nf-core#5278) added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158 (nf-core#5197) Update glimpse/phase output channel to phased_variants nf-core#5172 (nf-core#5174) Add module: GTFSORT (nf-core#5237) add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221) addedd optional output channel for lib files (nf-core#5257)
jvfe · Mar 19, 2024 · e16f6f9 · e16f6f9
2 parents 8402805 + cabcc0d
commit e16f6f9
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Showing 43 changed files with 2,416 additions and 1,844 deletions.
diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test b/modules/nf-core/bedtools/sort/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process BEDTOOLS_SORT"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "BEDTOOLS_SORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/sort"
+
+    test("test_bedtools_sort") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'],
+                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+
+    test("test_bedtools_sort_with_genome") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'],
+                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test.snap b/modules/nf-core/bedtools/sort/tests/main.nf.test.snap
diff --git a/modules/nf-core/bedtools/sort/tests/nextflow.config b/modules/nf-core/bedtools/sort/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    withName: BEDTOOLS_SORT {
+            ext.prefix = { "${meta.id}_out" }
+            ext.suffix = "testtext"
+    }
+
+}
diff --git a/modules/nf-core/bedtools/sort/tests/tags.yml b/modules/nf-core/bedtools/sort/tests/tags.yml
@@ -0,0 +1,2 @@
+bedtools/sort:
+  - "modules/nf-core/bedtools/sort/**"
diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/glimpse/concordance/meta.yml b/modules/nf-core/glimpse/concordance/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test b/modules/nf-core/glimpse/concordance/tests/main.nf.test
@@ -3,10 +3,13 @@ nextflow_process {
     name "Test Process GLIMPSE_CONCORDANCE"
     script "../main.nf"
     process "GLIMPSE_CONCORDANCE"
-    tag "glimpse"
-    tag "glimpse/concordance"
+
     tag "modules"
     tag "modules_nfcore"
+    tag "glimpse"
+    tag "glimpse/concordance"
+    tag "glimpse/phase"
+    tag "bcftools/index"
 
     test("test_glimpse_concordance") {
         setup {
@@ -20,15 +23,15 @@ nextflow_process {
                 ])
                 input_vcf     = Channel.of([
                     [ id:'input'], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
                 ])
                 ref_panel     = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
                 ])
                 ch_map        = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
                 ])
 
                 input[0]      = input_vcf
@@ -43,7 +46,7 @@ nextflow_process {
                 script "../../../bcftools/index/main.nf"
                 process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
                 }
             }
@@ -52,14 +55,14 @@ nextflow_process {
             process {
                 """
                 allele_freq = Channel.fromList([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
                 ]).collect()
                 truth = Channel.fromList([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
                 ]).collect()
-                estimate = GLIMPSE_PHASE.out.phased_variant
+                estimate = GLIMPSE_PHASE.out.phased_variants
                     | join (BCFTOOLS_INDEX.out.csi)
                 input[0] = estimate
                     | combine (allele_freq)

diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap b/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test b/modules/nf-core/glimpse/ligate/tests/main.nf.test
@@ -3,10 +3,13 @@ nextflow_process {
     name "Test Process GLIMPSE_LIGATE"
     script "../main.nf"
     process "GLIMPSE_LIGATE"
-    tag "glimpse"
-    tag "glimpse/ligate"
+
     tag "modules_nfcore"
     tag "modules"
+    tag "glimpse"
+    tag "glimpse/ligate"
+    tag "glimpse/phase"
+    tag "bcftools/index"
 
     test("test_glimpse_ligate") {
         setup {
@@ -21,15 +24,15 @@ nextflow_process {
                 ])
                 input_vcf     = Channel.of([
                     [ id:'input'], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
                 ])
                 ref_panel     = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
                 ])
                 ch_map        = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
                 ])
 
                 input[0]      = input_vcf
@@ -44,7 +47,7 @@ nextflow_process {
                 script "../../../bcftools/index/main.nf"
                 process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
                 }
             }
@@ -53,7 +56,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                     | groupTuple()
                     | join (BCFTOOLS_INDEX.out.csi.groupTuple())
                 """
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		bedtools/sort:
		- "modules/nf-core/bedtools/sort/**"