Update glimpse/phase output channel to phased_variants #5172

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

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

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)

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

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())
                 """

modules/nf-core/glimpse/phase/main.nf

@@ -4,14 +4,14 @@ process GLIMPSE_PHASE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
+        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
 
     input:
         tuple val(meta) , path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
 
     output:
-        tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variant
+        tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variants
         path "versions.yml"                               , emit: versions
 
     when:

modules/nf-core/glimpse/phase/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

modules/nf-core/glimpse/phase/tests/main.nf.test

@@ -22,15 +22,15 @@ 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
@@ -47,7 +47,7 @@ nextflow_process {
 
         then {
             String targetFileName = "input_present_chr21_16650000-16800000.vcf.gz"
-            File selectedFile = process.out.phased_variant.stream()
+            File selectedFile = process.out.phased_variants.stream()
                 .filter(vector -> vector.size() > 1)
                 .map(vector -> new File(vector.get(1).toString()))
                 .filter(file -> file.getName().equals(targetFileName))
@@ -58,7 +58,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.versions).match("versions") },
-                { assert process.out.phased_variant.size() == 4},
+                { assert process.out.phased_variants.size() == 4},
                 { assert snapshot(lines).match("imputed") }
             )
         }

modules/nf-core/glimpse/sample/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
@@ -22,12 +22,6 @@ input:
       type: file
       description: VCF/BCF file generated using GLIMPSE ligate
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-  - sample:
-      type: parameter
-      description: Samples a likely haplotype pair for each sample, use it in combination with --seed. Option not recommended for general usage, use --solve instead
-  - solve:
-      type: parameter
-      description: Get the most likely haplotype pair for each sample (the random number generator is not used)
 output:
   - meta:
       type: map

modules/nf-core/glimpse/sample/tests/main.nf.test

@@ -3,10 +3,12 @@ nextflow_process {
     name "Test Process GLIMPSE_SAMPLE"
     script "../main.nf"
     process "GLIMPSE_SAMPLE"
-    tag "glimpse"
-    tag "glimpse/sample"
+
     tag "modules"
     tag "modules_nfcore"
+    tag "glimpse"
+    tag "glimpse/sample"
+    tag "glimpse/phase"
 
     test("test_glimpse_sample") {
         config "./nextflow.config"
@@ -21,15 +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
@@ -44,7 +46,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
             }
         }

subworkflows/nf-core/vcf_impute_glimpse/main.nf

@@ -33,11 +33,11 @@ workflow VCF_IMPUTE_GLIMPSE {
     GLIMPSE_PHASE ( phase_input ) // [meta, vcf, index, sample_infos, regionin, regionout, ref, ref_index, map]
     ch_versions = ch_versions.mix(GLIMPSE_PHASE.out.versions )
 
-    INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variant )
+    INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variants )
     ch_versions = ch_versions.mix( INDEX_PHASE.out.versions )
 
     // Ligate all phased files in one and index it
-    ligate_input = GLIMPSE_PHASE.out.phased_variant
+    ligate_input = GLIMPSE_PHASE.out.phased_variants
         .groupTuple( by: 0 )
         .combine( INDEX_PHASE.out.csi
             .groupTuple( by: 0 ),