Merge branch 'master' into das_tool

nf-core · Dec 10, 2024 · 0599b7c · 0599b7c
2 parents f07910d + 9e13262
commit 0599b7c
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Showing 17 changed files with 358 additions and 48 deletions.
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -108,13 +108,18 @@ jobs:
     needs: [nf-test-gpu]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -32,7 +32,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -110,13 +110,18 @@ jobs:
     needs: [nf-test]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test
@@ -117,5 +117,4 @@ nextflow_process {
             )
         }
     }
-
 }
diff --git a/modules/nf-core/foldmason/msa2lddtreport/environment.yml b/modules/nf-core/foldmason/msa2lddtreport/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::foldmason=2.7bd21ed
diff --git a/modules/nf-core/foldmason/msa2lddtreport/main.nf b/modules/nf-core/foldmason/msa2lddtreport/main.nf
@@ -0,0 +1,52 @@
+process FOLDMASON_MSA2LDDTREPORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+    input:
+    tuple val(meta) , path(msa)
+    tuple val(meta2), path(db)
+    tuple val(meta3), path(pdbs)
+    tuple val(meta4), path(tree)
+
+    output:
+    tuple val(meta), path("${prefix}.html"), emit: html
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def options_tree = tree ? "--guide-tree $tree" : ""
+    """
+    foldmason msa2lddtreport \\
+        ${meta.id} \\
+        ${msa} \\
+        ${prefix}.html \\
+        $args \\
+        ${options_tree} \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/foldmason/msa2lddtreport/meta.yml b/modules/nf-core/foldmason/msa2lddtreport/meta.yml
@@ -0,0 +1,74 @@
+name: "foldmason_msa2lddtreport"
+description: Renders a visualization report using foldmason
+keywords:
+  - alignment
+  - MSA
+  - genomics
+  - structure
+tools:
+  - "foldmason":
+      description: "Multiple Protein Structure Alignment at Scale with FoldMason"
+      homepage: "https://github.com/steineggerlab/foldmason"
+      documentation: "https://github.com/steineggerlab/foldmason"
+      tool_dev_url: "https://github.com/steineggerlab/foldmason"
+      doi: "10.1101/2024.08.01.606130"
+      licence: ["GPL v3"]
+      identifier: biotools:foldmason
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - msa:
+        type: file
+        description: Input alignment file.
+        pattern: "*.{fa,fasta,aln}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - db:
+        type: file
+        description: Input foldmason database.
+        pattern: "*"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - pdbs:
+        type: file
+        description: Protein structures used for the visualization.
+        pattern: "*.{pdb}"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - tree:
+        type: file
+        description: Guide tree used for the visualization .
+        pattern: "*.{nwk,dnd}"
+output:
+  - html:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}.html":
+          type: file
+          description: HTML file with the foldmason visualization
+          pattern: "*.{html}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@luisas"
+maintainers:
+  - "@luisas"
diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process FOLDMASON_MSA2LDDTREPORT"
+    script "../main.nf"
+    process "FOLDMASON_MSA2LDDTREPORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "foldmason"
+    tag "foldmason/msa2lddtreport"
+    tag "foldmason/createdb"
+    tag "untar"
+    tag "famsa/guidetree"
+
+
+    setup{
+        run("UNTAR") {
+            script "../../../../../modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                    input[0] = Channel.of(tuple([id:'test'], archive))
+                    """
+                }
+        }
+
+        run("FAMSA_GUIDETREE") {
+            script "../../../../../modules/nf-core/famsa/guidetree/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_tree' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        run("FOLDMASON_CREATEDB") {
+            script "../../../../../modules/nf-core/foldmason/createdb/main.nf"
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+
+    }
+
+    test("seatoxin") {
+
+
+        when {
+            process {
+                """
+                input[0] =[ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]}
+                input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("seatixin - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =[ [ id:'test_tree' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]}
+                input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "seatixin - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_tree"
+                        },
+                        "test_tree.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test_tree"
+                        },
+                        "test_tree.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:36:23.360594258"
+    },
+    "seatoxin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,7a90a8e674dc45ce4181498b8f53b519"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,7a90a8e674dc45ce4181498b8f53b519"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:54:03.711567262"
+    }
+}
diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf
@@ -25,7 +25,7 @@ process MEGAHIT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
+    def reads_command = meta.single_end || !reads2 ? "-r ${reads1.join(',')}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
     """
     megahit \\
         ${reads_command} \\

diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ngs-bits=2023_02
+  - bioconda::ngs-bits=2024_11
-Original file line number
+Diff line change
@@ Expand Up / @@ -117,5 +117,4 @@ nextflow_process { @@
                 )
             }
         }
     }