bcftools isec input can be bcf or bcf.gz as well as vcf.gz

modules/nf-core/bcftools/isec/main.nf

@@ -11,8 +11,8 @@ process BCFTOOLS_ISEC {
     tuple val(meta), path(vcfs), path(tbis)
 
     output:
-    tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
+    tuple val(meta), path("${prefix}", type: "dir"), emit: results
+    path  "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,7 +24,25 @@ process BCFTOOLS_ISEC {
     bcftools isec  \\
         $args \\
         -p $prefix \\
-        *.vcf.gz
+        ${vcfs}
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}/README.txt
+    touch ${prefix}/sites.txt
+    echo "" | gzip > ${prefix}/0000.vcf.gz
+    touch ${prefix}/0000.vcf.gz.tbi
+    echo "" | gzip > ${prefix}/0001.vcf.gz
+    touch ${prefix}/0001.vcf.gz.tbi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')

modules/nf-core/bcftools/isec/meta.yml

@@ -6,6 +6,7 @@ keywords:
   - union
   - complement
   - VCF
+  - BCF
 tools:
   - isec:
       description: |
@@ -23,12 +24,12 @@ input:
   - vcfs:
       type: list
       description: |
-        List containing 2 or more vcf files
-        e.g. [ 'file1.vcf', 'file2.vcf' ]
+        List containing 2 or more vcf/bcf files. These must be compressed and have an associated index.
+        e.g. [ 'file1.vcf.gz', 'file2.vcf' ]
   - tbis:
       type: list
       description: |
-        List containing the tbi index files corresponding to the vcfs input files
+        List containing the tbi index files corresponding to the vcf/bcf input files
         e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
 output:
   - meta:

modules/nf-core/bcftools/isec/tests/main.nf.test

@@ -11,31 +11,69 @@ nextflow_process {
 
     config "./nextflow.config"
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") {
+    test("sarscov2 - [[vcf1.gz, vcf2.gz], [tbi1, tbi2]]") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)],
+                        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.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                        ]
                     ]
                 """
             }
         }
 
         then {
+            def results_dir = new File(process.out.results[0][1])
+            def results_list = []
+            results_dir.eachFileRecurse { file -> results_list << file.getName() }
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.results.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.versions
-                ).match() }
+                    process.out.versions,
+                    results_list.sort(),
+                    path("${process.out.results[0][1]}").list().findAll {
+                        it.getFileName().toString() != "0000.vcf.gz.tbi" && it.getFileName().toString() != "0001.vcf.gz.tbi"
+                    }
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // 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/test.vcf.gz.tbi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                        ]
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 

modules/nf-core/bcftools/isec/tests/main.nf.test.snap

@@ -1,22 +1,75 @@
 {
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": {
+    "sarscov2 - [[vcf1.gz, vcf2.gz], [tbi1, tbi2]]": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test"
-                ]
+                "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
             ],
             [
-                "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                "0000.vcf.gz",
+                "0000.vcf.gz.tbi",
+                "0001.vcf.gz",
+                "0001.vcf.gz.tbi",
+                "README.txt",
+                "sites.txt"
+            ],
+            [
+                "0000.vcf.gz:md5,8e722884ffb75155212a3fc053918766",
+                "0001.vcf.gz:md5,b39a72f91458b94b346dd73690207649",
+                "README.txt:md5,10fc33b66522645600d44afbd41fb792",
+                "sites.txt:md5,1cea3fbde7f6d3c97f3d39036f9690df"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:43:55.820868944"
+        "timestamp": "2024-07-03T16:32:18.167072863"
+    },
+    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "0000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "0001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "0001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "README.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "0000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "0001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "0001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "README.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T09:45:52.881120953"
     }
 }