DO NOT MERGE update fasta_index_dna

subworkflows/nf-core/fasta_index_dna/main.nf

@@ -22,50 +22,41 @@ workflow FASTA_INDEX_DNA {
     ch_aligner_index    = Channel.empty()
     ch_versions         = Channel.empty()
 
-    switch (val_aligner) {
-        case 'bowtie2':
-            BOWTIE2_BUILD(ch_fasta )                                             // if aligner is bowtie2
-            ch_aligner_index = ch_aligner_index.mix(BOWTIE2_BUILD.out.index)
-            ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
-            break
-        case 'bwamem':
-            BWAMEM1_INDEX(ch_fasta)                                              // If aligner is bwa-mem
-            ch_aligner_index = ch_aligner_index
-                .mix(
-                    BWAMEM1_INDEX.out.index
-                    .join(ch_altliftover)
-                    .map{meta, index, alt -> [meta, index + alt]}
-                )
+    // Handle different aligners using conditional logic
+    if (val_aligner == 'bowtie2') {
+        BOWTIE2_BUILD(ch_fasta)
+        ch_aligner_index = BOWTIE2_BUILD.out.index
+        ch_versions = BOWTIE2_BUILD.out.versions
+    } else if (val_aligner == 'bwamem') {
+        BWAMEM1_INDEX(ch_fasta)
 
-            ch_versions = ch_versions.mix(BWAMEM1_INDEX.out.versions)
-            break
-        case 'bwamem2':
-            BWAMEM2_INDEX(ch_fasta)                                              // If aligner is bwa-mem2
-            ch_aligner_index = ch_aligner_index
-                .mix(
-                    BWAMEM2_INDEX.out.index
-                    .join(ch_altliftover)
-                    .map{meta, index, alt -> [meta, index + alt]}
-                )
+        // returning the alt file next to the index, not inside the folder
+        ch_aligner_index = BWAMEM1_INDEX.out.index
+            .join(ch_altliftover)
+            .map { meta, index, alt -> [meta, [index, alt] ] }
+        ch_versions = BWAMEM1_INDEX.out.versions
+    } else if (val_aligner == 'bwamem2') {
+        BWAMEM2_INDEX(ch_fasta)
+        // returning the alt file next to the index, not inside the folder
+        ch_aligner_index = BWAMEM2_INDEX.out.index
+            .join(ch_altliftover)
+            .map { meta, index, alt -> [meta, [index, alt] ] }
 
-            ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
-            break
-        case 'dragmap':
-            DRAGMAP_HASHTABLE(ch_fasta)                                          // If aligner is dragmap
-            ch_aligner_index = ch_aligner_index.mix(DRAGMAP_HASHTABLE.out.hashmap)
-            ch_versions = ch_versions.mix(DRAGMAP_HASHTABLE.out.versions)
-            break
-        case 'snap':
-            ch_snap_reference = ch_fasta
-                .join(ch_altliftover)
-                .map {meta, fasta, alt -> [meta, fasta, [], [], alt]}
+        ch_versions = BWAMEM2_INDEX.out.versions
+    } else if (val_aligner == 'dragmap') {
+        DRAGMAP_HASHTABLE(ch_fasta)
+        ch_aligner_index = DRAGMAP_HASHTABLE.out.hashmap
+        ch_versions = DRAGMAP_HASHTABLE.out.versions
+    } else if (val_aligner == 'snap') {
+        ch_snap_reference = ch_fasta
+            .join(ch_altliftover)
+            .map { meta, fasta_, alt -> [meta, fasta_, [], [], alt] }
 
-            SNAP_INDEX(ch_snap_reference)                                        // If aligner is snap
-            ch_aligner_index = ch_aligner_index.mix(SNAP_INDEX.out.index)
-            ch_versions = ch_versions.mix(SNAP_INDEX.out.versions)
-            break
-        default:
-            error "Unknown aligner: ${val_aligner}"
+        SNAP_INDEX(ch_snap_reference)
+        ch_aligner_index = SNAP_INDEX.out.index
+        ch_versions = SNAP_INDEX.out.versions
+    } else {
+        error "Unknown aligner: ${val_aligner}"
     }
 
     emit:

subworkflows/nf-core/fasta_index_dna/tests/main.nf.test

@@ -0,0 +1,289 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTA_INDEX_DNA"
+    script "../main.nf"
+    workflow "FASTA_INDEX_DNA"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fasta_index_dna"
+    tag "bowtie2/build"
+    tag "bwa/index"
+    tag "bwamem2/index"
+    tag "dragmap/hashtable"
+    tag "snapaligner/index"
+
+    test("Params: bowtie2 | generate bowtie2 index") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bowtie2'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: bwamem | generate bwamem1 index") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bwamem'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: bwamem2 | generate bwamem2 index") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bwamem2'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: dragmap | generate dragmap hashtable") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'dragmap'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out.index[1].collect { file(it).name }.toSorted(),
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: snapaligner | generate snapaligner index") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'snap'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out.index[0][1].collect { file(it).name }.toSorted(),
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+
+
+    test("Params: bowtie2 | generate bowtie2 index - stub") {
+        options '-stub'
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bowtie2'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: bwamem | generate bwamem1 index - stub") {
+        options '-stub'
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bwamem'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: bwamem2 | generate bwamem2 index - stub") {
+        options '-stub'
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'bwamem2'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: dragmap | generate dragmap hashtable - stub") {
+        options '-stub'
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'dragmap'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+    test("Params: snapaligner | generate snapaligner index - stub") {
+        options '-stub'
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    ])
+                input[1] = Channel.value([
+                    [id:'test'],
+                    []
+                    ])
+                input[2] = 'snap'
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+
+}