Merge branch 'master' into gzrt

nf-core · Jan 7, 2025 · e0ed20b · e0ed20b
2 parents 1784542 + cb8e4c9
commit e0ed20b
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diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
       with:
         distribution: "temurin"
         java-version: "17"

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -120,7 +120,7 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -258,7 +258,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"
@@ -308,7 +308,7 @@ jobs:
 
       - name: Upload logs on failure
         if: failure()
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
         with:
           name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
           path: |

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false

diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
@@ -10,6 +10,7 @@ process BCFTOOLS_ANNOTATE {
     input:
     tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
     path(header_lines)
+    path(rename_chrs)
 
     output:
     tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
@@ -25,6 +26,7 @@ process BCFTOOLS_ANNOTATE {
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def header_file = header_lines ? "--header-lines ${header_lines}" : ''
     def annotations_file = annotations ? "--annotations ${annotations}" : ''
+    def rename_chrs_file = rename_chrs ? "--rename-chrs ${rename_chrs}" : ''
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
@@ -40,6 +42,7 @@ process BCFTOOLS_ANNOTATE {
         annotate \\
         $args \\
         $annotations_file \\
+        $rename_chrs_file \\
         $header_file \\
         --output ${prefix}.${extension} \\
         --threads $task.cpus \\

diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml
@@ -35,6 +35,9 @@ input:
   - - header_lines:
         type: file
         description: Contains lines to append to the output VCF header
+  - - rename_chrs:
+        type: file
+        description: Rename annotations according to this file containing "old_name new_name\n" pairs separated by whitespaces, each on a separate line.
 output:
   - vcf:
       - meta:

diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test
@@ -9,7 +9,7 @@ nextflow_process {
     tag "bcftools"
     tag "bcftools/annotate"
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output") {
 
         config "./vcf.config"
 
@@ -24,6 +24,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -40,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output") {
 
         config "./vcf.config"
 
@@ -55,6 +56,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -70,7 +72,7 @@ nextflow_process {
         }
 
     }
-        test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") {
+        test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
@@ -85,6 +87,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -104,7 +107,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
@@ -119,6 +122,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -138,7 +142,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
@@ -153,6 +157,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -171,7 +176,8 @@ nextflow_process {
         }
 
     }
-    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") {
+
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, [] - bcf_output") {
 
         config "./bcf.config"
 
@@ -189,6 +195,7 @@ nextflow_process {
                     '##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">',
                     '##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">'
                 ).collectFile(name:"headers.vcf", newLine:true)
+                input[2] = []
                 """
             }
         }
@@ -205,7 +212,43 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index") {
+
+        config "./vcf_gz_index.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    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] = Channel.of(
+                    '##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">',
+                    '##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">'
+                ).collectFile(name:"headers.vcf", newLine:true)
+                input[2] = Channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).LinesGzip.contains("##contig=<ID=renamed,length=29829>")},
+                { assert snapshot(
+                    process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub") {
 
         config "./vcf.config"
         options "-stub"
@@ -221,6 +264,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -234,7 +278,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -250,6 +294,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -264,7 +309,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -280,6 +325,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -294,7 +340,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"
@@ -310,6 +356,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }