Merge branch 'master' into nf-test/gfaffix

nf-core · Sep 6, 2024 · ced792c · ced792c
2 parents ccfd9dd + 6f2dfbf
commit ced792c
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Showing 75 changed files with 2,021 additions and 2,408 deletions.
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
@@ -24,7 +24,8 @@ process BCFTOOLS_MERGE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input = vcfs.sort{ it.name }
+
+    def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs
     def regions = bed ? "--regions-file $bed" : ""
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :

diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test
@@ -244,6 +244,7 @@ nextflow_process {
         config "./vcf_gz_index_csi.config"
 
         when {
+
             process {
                 """
                 input[0] = [
@@ -363,6 +364,7 @@ nextflow_process {
     test("homo_sapiens - [vcf, tbi], fasta, fai, bed  - vcf.gz output") {
 
         config "./nextflow.gvcf.config"
+
         when {
             process {
                 """
@@ -406,6 +408,41 @@ nextflow_process {
 
     }
 
+    test("sarscov2 - [vcf, tbi], [], [], [] - one sample") {
+
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                    ]
+                ]
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.vcf.get(0).get(1).endsWith("vcf") },
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).md5,
+                    process.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
     test("sarscov2 - [vcf, tbi], [], [], [] - stub") {
 
         options "-stub"
@@ -779,4 +816,38 @@ nextflow_process {
         }
 
     }
+
+    test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                    ]
+                ]
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.vcf.get(0).get(1).endsWith("vcf") },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 }
diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap
@@ -372,6 +372,45 @@
         },
         "timestamp": "2024-09-05T13:17:47.356328326"
     },
+    "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                ],
+                "index": [
+
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T15:13:18.708495878"
+    },
     "homo_sapiens - [vcf, tbi], fasta, fai, bed  - vcf.gz output - stub": {
         "content": [
             {
@@ -438,6 +477,19 @@
         },
         "timestamp": "2024-09-05T13:55:44.299812124"
     },
+    "sarscov2 - [vcf, tbi], [], [], [] - one sample": {
+        "content": [
+            "2a374cf02f0c32cf607646167e7f153b",
+            [
+                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T15:37:38.491844702"
+    },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             {

diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: BCFTOOLS_MERGE {
-        ext.args = '--force-samples --no-version'
+        ext.args = '--force-samples --force-single --no-version'
     }
 }
diff --git a/modules/nf-core/circexplorer2/parse/environment.yml b/modules/nf-core/circexplorer2/parse/environment.yml
@@ -2,6 +2,5 @@ name: circexplorer2_parse
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::circexplorer2=2.3.8
diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/YangLab/CIRCexplorer2/"
       documentation: "https://circexplorer2.readthedocs.io/en/latest/"
       doi: "10.1101/gr.202895.115"
-      licence: "['MIT License']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test b/modules/nf-core/circexplorer2/parse/tests/main.nf.test
@@ -0,0 +1,62 @@
+
+nextflow_process {
+
+    name "Test Process CIRCEXPLORER2_PARSE"
+    script "../main.nf"
+    process "CIRCEXPLORER2_PARSE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "circexplorer2"
+    tag "circexplorer2/parse"
+
+    test("test-circexplorer2-parse") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'fust1_3' ],
+				    file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction")
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.junction[0][1]).text.contains('FUSIONJUNC') },
+                { assert snapshot(
+                    file(process.out.junction[0][1]).name, // unstable
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-circexplorer2-parse-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'fust1_3' ],
+				    file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction")
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap b/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "test-circexplorer2-parse-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "fust1_3"
+                        },
+                        "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6490a204cc08154871418e5fbb3aff17"
+                ],
+                "junction": [
+                    [
+                        {
+                            "id": "fust1_3"
+                        },
+                        "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6490a204cc08154871418e5fbb3aff17"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:58:38.034614"
+    },
+    "test-circexplorer2-parse": {
+        "content": [
+            "fust1_3.bed",
+            [
+                "versions.yml:md5,6490a204cc08154871418e5fbb3aff17"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:53:55.470118"
+    }
+}
diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml
@@ -2,6 +2,6 @@ name: geoquery_getgeo
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::bioconductor-geoquery=2.66.0
+  - bioconda::bioconductor-geoquery=2.70.0
+  - conda-forge::r-base=4.3.2 # Locked with container
diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf
@@ -4,8 +4,8 @@ process GEOQUERY_GETGEO {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.66.0--r42hdfd78af_0' :
-        'biocontainers/bioconductor-geoquery:2.66.0--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.70.0--r43hdfd78af_0' :
+        'biocontainers/bioconductor-geoquery:2.70.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), val(querygse)
@@ -21,4 +21,18 @@ process GEOQUERY_GETGEO {
 
     script:
     template 'getgeo.R'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.rds
+    touch ${prefix}.matrix.tsv
+    touch ${prefix}.annotation.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(Rscript -e 'R.Version()\$version.string' | sed -n 's|\\[1\\] "R version \\(.*\\) (.*|\\1|p')
+        bioconductor-geoquery: \$(Rscript -e 'packageVersion("GEOquery")' | sed -n 's|\\[1\\] ‘\\(.*\\)’|\\1|p')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html"
       tool_dev_url: "https://github.com/seandavi/GEOquery"
       doi: "10.1093/bioinformatics/btm254"
-      licence: "MIT"
+      licence: ["MIT"]
 input:
   - meta:
       type: map