Merge branch 'master' into shapeit5_phaserare

nf-core · Dec 4, 2024 · 532f301 · 532f301
2 parents 08a702c + 175e642
commit 532f301
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diff --git a/modules/nf-core/shapeit5/ligate/environment.yml b/modules/nf-core/shapeit5/ligate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::shapeit5=1.0.0
+  - bioconda::shapeit5=5.1.1
diff --git a/modules/nf-core/shapeit5/ligate/main.nf b/modules/nf-core/shapeit5/ligate/main.nf
@@ -4,11 +4,11 @@ process SHAPEIT5_LIGATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/shapeit5:1.0.0--h0c8ee15_0':
-        'biocontainers/shapeit5:1.0.0--h0c8ee15_0'}"
+        'https://depot.galaxyproject.org/singularity/shapeit5:5.1.1--hb60d31d_0':
+        'biocontainers/shapeit5:5.1.1--hb60d31d_0'}"
 
     input:
-    tuple val(meta), path(input_list), path (input_list_index)
+    tuple val(meta), path(input_list), path(input_list_index)
 
     output:
     tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: merged_variants
@@ -37,11 +37,11 @@ process SHAPEIT5_LIGATE {
     """
 
     stub:
-    def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "vcf.gz"
+    def prefix     = task.ext.prefix        ?: "${meta.id}"
+    def suffix     = task.ext.suffix        ?: "vcf.gz"
+    def create_cmd = suffix.endsWith(".gz") ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${suffix}
+    ${create_cmd} ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/shapeit5/ligate/tests/main.nf.test b/modules/nf-core/shapeit5/ligate/tests/main.nf.test
@@ -0,0 +1,99 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_LIGATE"
+    script "../main.nf"
+    process "SHAPEIT5_LIGATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/ligate"
+    tag "bcftools/view"
+
+    test("homo sapiens - map, [vcf], [tbi]") {
+        config "./nextflow.config"
+        setup {
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_1") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr22:16570000-16600000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_1' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_2") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr22:16580000-16610000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_2' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_VIEW_1.out.vcf.join(BCFTOOLS_VIEW_1.out.csi)
+                    .mix(BCFTOOLS_VIEW_2.out.vcf.join(BCFTOOLS_VIEW_2.out.csi))
+                    .map { meta, vcf, csi -> [ [id : "NA12878"], vcf, csi ] }
+                    .groupTuple()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.merged_variants.collect {meta, vcf -> [ meta, path(vcf).vcf.summary ]},
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - map, [vcf], [tbi] - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'NA12878'],
+                    [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true)],
+                    [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true)]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap b/modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "homo sapiens - map, [vcf], [tbi] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ],
+                "merged_variants": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T17:22:34.235879155"
+    },
+    "homo sapiens - map, [vcf], [tbi]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "NA12878"
+                    },
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=60, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-04T10:07:53.185018802"
+    }
+}
diff --git a/modules/nf-core/shapeit5/ligate/tests/nextflow.config b/modules/nf-core/shapeit5/ligate/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: "BCFTOOLS_VIEW_*" {
+        ext.args = params.bcftools_args
+        ext.prefix = { "${meta.id}" }
+    }
+}
diff --git a/modules/nf-core/shapeit5/switch/environment.yml b/modules/nf-core/shapeit5/switch/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::shapeit5=1.0.0
+  - bioconda::shapeit5=5.1.1
diff --git a/modules/nf-core/shapeit5/switch/main.nf b/modules/nf-core/shapeit5/switch/main.nf
@@ -4,8 +4,8 @@ process SHAPEIT5_SWITCH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/shapeit5:1.0.0--h0c8ee15_0':
-        'biocontainers/shapeit5:1.0.0--h0c8ee15_0'}"
+        'https://depot.galaxyproject.org/singularity/shapeit5:5.1.1--hb60d31d_0':
+        'biocontainers/shapeit5:5.1.1--hb60d31d_0'}"
 
     input:
         tuple val(meta) , path(estimate), path(estimate_index), val(region), path(pedigree)
@@ -43,18 +43,18 @@ process SHAPEIT5_SWITCH {
     """
 
     stub:
-    def args         = task.ext.args   ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
+    def create_cmd   = "echo '' | gzip >"
     """
-    touch ${prefix}.block.switch.txt.gz
-    touch ${prefix}.calibration.switch.txt.gz
-    touch ${prefix}.flipsAndSwitches.txt.gz
-    touch ${prefix}.frequency.switch.txt.gz
-    touch ${prefix}.sample.switch.txt.gz
-    touch ${prefix}.sample.typing.txt.gz
-    touch ${prefix}.type.switch.txt.gz
-    touch ${prefix}.variant.switch.txt.gz
-    touch ${prefix}.variant.typing.txt.gz
+    ${create_cmd} ${prefix}.block.switch.txt.gz
+    ${create_cmd} ${prefix}.calibration.switch.txt.gz
+    ${create_cmd} ${prefix}.flipsAndSwitches.txt.gz
+    ${create_cmd} ${prefix}.frequency.switch.txt.gz
+    ${create_cmd} ${prefix}.sample.switch.txt.gz
+    ${create_cmd} ${prefix}.sample.typing.txt.gz
+    ${create_cmd} ${prefix}.type.switch.txt.gz
+    ${create_cmd} ${prefix}.variant.switch.txt.gz
+    ${create_cmd} ${prefix}.variant.typing.txt.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/shapeit5/switch/tests/main.nf.test b/modules/nf-core/shapeit5/switch/tests/main.nf.test
@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_SWITCH"
+    script "../main.nf"
+    process "SHAPEIT5_SWITCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/switch"
+    tag "shapeit5/phasecommon"
+    tag "bcftools/index"
+
+    test("homo sapiens - vcf, scaffold, []") {
+        config "./nextflow.config"
+        setup {
+            run("SHAPEIT5_PHASECOMMON") {
+                script "../../../shapeit5/phasecommon"
+                params {
+                    shapeit5_phasecommon_args = "--filter-maf 0.001"
+                }
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'scaffold', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists: true),
+                        [],
+                        "chr22",
+                    ])
+                    input[1] = Channel.of([[],[],[]])
+                    input[2] = Channel.of([[],[],[]])
+                    input[3] = Channel.of([[],[]])
+                    """
+                }
+            }
+            run("BCFTOOLS_INDEX") {
+                script "../../../bcftools/index"
+                process {
+                    """
+                    input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant
+                    .join(BCFTOOLS_INDEX.out.csi)
+                    .combine(Channel.of("chr22"))
+                    .combine(Channel.of([[]]))
+                input[1] = Channel.of([[ id:'truth_panel'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi",checkIfExists:true)
+                ])
+                input[2] = Channel.of([[ id:'freq_file'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz.csi",checkIfExists:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.errors.collect { meta, txt -> [ meta, txt.collect{ file(it).name } ] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf, scaffold, [] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'truth_panel'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi",checkIfExists:true),
+                    "chr21",
+                    []
+                ])
+                input[1] = [[], [], []]
+                input[2] = [[], [], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}