use conda-forge instead of anaconda (#5626)

* use conda-forge instead of anaconda * Update modules/nf-core/homer/maketagdirectory/environment.yml Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * nf-test homer/findpeaks * nf-test homer/maketagdirectory * nf-test homer/pos2bed * fix perl version? * Update modules/nf-core/gawk/environment.yml Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * fix gawk --------- Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
nf-core · May 17, 2024 · cf3ed07 · cf3ed07
1 parent 7948029
commit cf3ed07
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Showing 28 changed files with 616 additions and 197 deletions.
diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml
@@ -5,5 +5,5 @@ channels:
   - defaults
 dependencies:
   - bioconda::cadd-scripts=1.6.post1
-  - anaconda::conda=4.14.0
+  - conda-forge::conda=4.14.0
   - conda-forge::mamba=1.4.0
diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - anaconda::gawk=5.1.0
+  - conda-forge::gawk=5.3.0
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
@@ -4,8 +4,8 @@ process GAWK {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'biocontainers/gawk:5.1.0' }"
+        'https://depot.galaxyproject.org/singularity/gawk:5.3.0' :
+        'biocontainers/gawk:5.3.0' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
                 ],
                 "output": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nextflow": "24.03.0"
         },
-        "timestamp": "2024-04-05T11:00:28.097563"
+        "timestamp": "2024-05-17T15:20:02.495430346"
     },
     "convert fasta to bed": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
                 ],
                 "output": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nextflow": "24.03.0"
         },
-        "timestamp": "2024-04-05T10:28:15.625869"
+        "timestamp": "2024-05-17T15:19:53.291809648"
     }
 }
diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf
@@ -34,4 +34,17 @@ process HOMER_FINDPEAKS {
         homer: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    touch ${prefix}.peaks.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/homer/findpeaks/tests/main.nf.test b/modules/nf-core/homer/findpeaks/tests/main.nf.test
@@ -0,0 +1,73 @@
+nextflow_process {
+
+    name "Test Process HOMER_FINDPEAKS"
+    script "../main.nf"
+    process "HOMER_FINDPEAKS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "homer"
+    tag "homer/findpeaks"
+    tag "homer/maketagdirectory"
+
+    setup {
+        run("HOMER_MAKETAGDIRECTORY") {
+            script "../../maketagdirectory/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+
+    }
+
+    test("sarscov2 - tagdir") {
+
+        when {
+            process {
+                """
+                input[0] = HOMER_MAKETAGDIRECTORY.out.tagdir
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("tagdir") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - tagdir - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = HOMER_MAKETAGDIRECTORY.out.tagdir
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/homer/findpeaks/tests/main.nf.test.snap b/modules/nf-core/homer/findpeaks/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.peaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,12c3e88a3eeb96208a1d352504ebebfa"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.peaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,12c3e88a3eeb96208a1d352504ebebfa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-17T13:57:52.208349083"
+    },
+    "tagdir": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.peaks.txt:md5,86e15beaa4b439585786478e58418c0c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,12c3e88a3eeb96208a1d352504ebebfa"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.peaks.txt:md5,86e15beaa4b439585786478e58418c0c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,12c3e88a3eeb96208a1d352504ebebfa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-17T13:56:22.119853182"
+    }
+}
diff --git a/...s/nf-core/homer/findpeaks/nextflow.config → ...ore/homer/findpeaks/tests/nextflow.config b/...s/nf-core/homer/findpeaks/nextflow.config → ...ore/homer/findpeaks/tests/nextflow.config
@@ -1,13 +1,8 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: HOMER_MAKETAGDIRECTORY {
         ext.args = '-format bed'
     }
-
     withName: HOMER_FINDPEAKS {
         ext.args = '-style factor'
     }
-
 }
diff --git a/modules/nf-core/homer/findpeaks/tests/tags.yml b/modules/nf-core/homer/findpeaks/tests/tags.yml
@@ -0,0 +1,2 @@
+homer/findpeaks:
+  - "modules/nf-core/homer/findpeaks/**"
diff --git a/modules/nf-core/homer/maketagdirectory/environment.yml b/modules/nf-core/homer/maketagdirectory/environment.yml
@@ -9,4 +9,4 @@ dependencies:
   - conda-forge::r-base=4.0.2
   - bioconda::bioconductor-deseq2=1.30.0
   - bioconda::bioconductor-edger=3.32.0
-  - anaconda::perl=5.26.2
+  - conda-forge::perl=5.26.2
diff --git a/modules/nf-core/homer/maketagdirectory/tests/bed.config b/modules/nf-core/homer/maketagdirectory/tests/bed.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = '-format bed'
+}
diff --git a/modules/nf-core/homer/maketagdirectory/tests/main.nf.test b/modules/nf-core/homer/maketagdirectory/tests/main.nf.test
@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process HOMER_MAKETAGDIRECTORY"
+    script "../main.nf"
+    process "HOMER_MAKETAGDIRECTORY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "homer"
+    tag "homer/maketagdirectory"
+
+    test("sarscov2 - [bed, bed], fasta") {
+
+        config "./bed.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("bed") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bam, bam], fasta") {
+
+        config "./sam.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("bam") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bed, bed], fasta - stub") {
+
+        config "./bed.config"
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("stub") }
+            )
+        }
+
+    }
+
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		homer/findpeaks:
		- "modules/nf-core/homer/findpeaks/**"