Merge branch 'master' of https://github.com/nf-core/modules into bump…

…_shinyngs_2.1.0
nf-core · Jan 17, 2025 · 7e71f5c · 7e71f5c
2 parents 2f32f10 + 0306f1e
commit 7e71f5c
Showing 82 changed files with 1,729 additions and 909 deletions.
diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
@@ -86,6 +86,8 @@
     "docker_self_hosted": ["modules/nf-core/parabricks"],
     "singularity": [
         "modules/nf-core/bases2fastq",
+        "modules/nf-core/deepvariant/rundeepvariant",
+        "modules/nf-core/deepvariant/vcfstatsreport",
         "modules/nf-core/deepsomatic",
         "modules/nf-core/parabricks",
         "modules/nf-core/universc"

diff --git a/modules/nf-core/custom/matrixfilter/main.nf b/modules/nf-core/custom/matrixfilter/main.nf
@@ -2,9 +2,9 @@ process CUSTOM_MATRIXFILTER {
     tag "$meta"
     label 'process_single'
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-base:4.2.1' :
-        'biocontainers/r-base:4.2.1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/483e9d9b3b07e5658792d579e230ad40ed18daf7b9ebfb4323c08570f92fd1d5/data'
+        : 'community.wave.seqera.io/library/r-base:4.2.1--b0b5476e2e7a0872'}"
 
     input:
     tuple val(meta), path(abundance)
@@ -13,7 +13,7 @@ process CUSTOM_MATRIXFILTER {
     output:
     tuple val(meta), path("*.filtered.tsv")             , emit: filtered
     tuple val(meta), path("*.tests.tsv")                , emit: tests
-    tuple val(meta), path("R_sessionInfo.log")          , emit: session_info
+    tuple val(meta), path("*R_sessionInfo.log")         , emit: session_info
     path "versions.yml"                                 , emit: versions
 
     when:
@@ -27,4 +27,17 @@ process CUSTOM_MATRIXFILTER {
     // (new variables defined here don't seem to be available in templates, so
     // we have to access $task directly)
     template 'matrixfilter.R'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.filtered.tsv
+    touch ${prefix}.tests.tsv
+    touch ${prefix}.R_sessionInfo.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/custom/matrixfilter/meta.yml b/modules/nf-core/custom/matrixfilter/meta.yml
@@ -62,7 +62,7 @@ output:
           description: |
             Groovy Map containing information on experiment.
             e.g. [ id:'test' ]
-      - R_sessionInfo.log:
+      - "*R_sessionInfo.log":
           type: file
           description: Log file containing R session information
           pattern: "*.log"

diff --git a/modules/nf-core/custom/matrixfilter/templates/matrixfilter.R b/modules/nf-core/custom/matrixfilter/templates/matrixfilter.R
@@ -207,7 +207,7 @@ keep <- apply(boolean_matrix, 1, all)
 # Write out the matrix retaining the specified rows and re-prepending the
 # column with the feature identifiers
 
-prefix = ifelse('$task.ext.prefix' == 'null', '', '$task.ext.prefix')
+prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix')
 
 write.table(
     data.frame(rownames(abundance_matrix)[keep], abundance_matrix[keep,,drop = FALSE]),

diff --git a/modules/nf-core/custom/matrixfilter/tests/main.nf.test b/modules/nf-core/custom/matrixfilter/tests/main.nf.test
@@ -0,0 +1,100 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_MATRIXFILTER"
+    script "../main.nf"
+    process "CUSTOM_MATRIXFILTER"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom_matrixfilter"
+    tag "custom"
+    tag "custom/matrixfilter"
+
+    test("test_custom_matrixfilter") {
+
+        when {
+            params {
+                observations_id_col             = 'sample'
+                filtering_min_samples           = 1.0
+                filtering_min_abundance         = 10
+                filtering_min_proportion        = null
+                filtering_grouping_var          = null
+                filtering_min_proportion_not_na = 0.5
+                filtering_min_samples_not_na    = null
+
+                module_args = [
+                    "--sample_id_col \"${params.observations_id_col}\"",
+                    "--minimum_samples ${params.filtering_min_samples}",
+                    "--minimum_abundance ${params.filtering_min_abundance}",
+                    (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''),
+                    (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''),
+                    (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''),
+                    (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '')
+                ].join(' ').trim()
+            }
+            process {
+                """
+                input[0] = [ [id:"test"],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true)
+                ]
+                input[1] = [ [id:"test"],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true)
+                ]
+                """
+
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.filtered,
+                process.out.tests,
+                process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_custom_matrixfilter - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                observations_id_col             = 'sample'
+                filtering_min_samples           = 1.0
+                filtering_min_abundance         = 10
+                filtering_min_proportion        = null
+                filtering_grouping_var          = null
+                filtering_min_proportion_not_na = 0.5
+                filtering_min_samples_not_na    = null
+                module_args   = [
+                    "--sample_id_col \"${params.observations_id_col}\"",
+                    "--minimum_samples ${params.filtering_min_samples}",
+                    "--minimum_abundance ${params.filtering_min_abundance}",
+                    (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''),
+                    (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''),
+                    (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''),
+                    (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '')
+                ].join(' ').trim()
+            }
+            process {
+                """
+                input[0] = [ [id:"test"],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true)
+                ]
+                input[1] = [ [id:"test"],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap b/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap
@@ -0,0 +1,95 @@
+{
+    "test_custom_matrixfilter": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2"
+                ]
+            ],
+            [
+                "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-13T21:21:11.862199262"
+    },
+    "test_custom_matrixfilter - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
+                ],
+                "filtered": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "session_info": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tests": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-13T21:22:31.144793503"
+    }
+}
diff --git a/modules/nf-core/custom/matrixfilter/tests/nextflow.config b/modules/nf-core/custom/matrixfilter/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = params.module_args
+}
diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf
@@ -40,7 +40,18 @@ process CUSTOM_TABULARTOGSEACLS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: \$(mawk -W version | head -n 1 | awk '{print  \$2}')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.cls
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        awk: \$(mawk -W version | head -n 1 | awk '{print  \$2}')
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test
@@ -0,0 +1,63 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_TABULARTOGSEACLS"
+    script "../main.nf"
+    process "CUSTOM_TABULARTOGSEACLS"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom_tabulartogseacls"
+    tag "custom"
+    tag "custom/tabulartogseacls"
+
+    test("test_custom_tabulartogseacls") {
+
+        when {
+            params {
+                module_args = [ "separator": "\t", "variable": "treatment" ]
+            }
+            process {
+                """
+                input[0] = [
+                    [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv", checkIfExists: true)
+                ]
+                """
+
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_tabulartogseacls - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = { [ "separator": "\t", "variable": "treatment" ] }
+            }
+            process {
+                """
+                input[0] = [
+                    [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'],
+                    file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}