Added Cram_qc_mosdepth_samtools to nf core subworkflows

subworkflows/nf-core/cram_qc_mosdepth_samtools/main.nf

@@ -0,0 +1,33 @@
+//
+// QC on CRAM
+//
+
+include { MOSDEPTH       } from '../../../modules/nf-core/mosdepth'
+include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats'
+
+workflow CRAM_QC_MOSDEPTH_SAMTOOLS {
+    take:
+    cram      // channel: [mandatory] [ meta, cram, crai ]
+    fasta_fai     // channel: [mandatory] [ meta, fasta, fai ]
+    intervals
+
+    main:
+    reports = channel.empty()
+
+    // Reports run on cram
+    SAMTOOLS_STATS(cram, fasta_fai)
+
+    ch_mosdepth_in = cram
+        .combine(intervals.map { meta, interval -> interval }.ifEmpty([ [] ]))
+        .map { meta, cram_file, crai, bed -> [ meta, cram_file, crai, bed ?: [] ] }
+
+    MOSDEPTH(ch_mosdepth_in, fasta_fai.map { meta, fasta, fai -> [ meta, fasta ] }, [])
+
+    // Gather all reports generated
+    reports = reports.mix(SAMTOOLS_STATS.out.stats)
+    reports = reports.mix(MOSDEPTH.out.global_txt)
+    reports = reports.mix(MOSDEPTH.out.regions_txt)
+
+    emit:
+    reports // channel: [ meta, report_file ]
+}

subworkflows/nf-core/cram_qc_mosdepth_samtools/meta.yml

@@ -0,0 +1,63 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: cram_qc_mosdepth_samtools
+description: Comprehensive QC analysis on CRAM files using mosdepth and samtools
+keywords:
+  - qc
+  - cram
+  - quality-control
+  - mosdepth
+  - samtools
+  - coverage
+  - statistics
+components:
+  - samtools/stats
+  - mosdepth
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample1', single_end:false ]
+  - cram:
+      type: file
+      description: CRAM file
+      pattern: "*.cram"
+  - crai:
+      type: file
+      description: CRAM file index
+      pattern: "*.crai"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fasta,fa,fna}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing interval information
+        e.g. [ id:'intervals' ]
+  - intervals:
+      type: optional file
+      description: BED file containing genomic intervals
+      pattern: "*.bed"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample1', single_end:false ]
+  - reports:
+      type: file
+      description: QC report files (samtools stats and mosdepth outputs)
+      pattern: "*{.stats,.txt,.bed.gz,.bed.gz.csi}"
+
+authors:
+  - "@agrima2010"
+maintainers:
+  - "@agrima2010"

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

@@ -0,0 +1,111 @@
+nextflow_workflow {
+
+    name "Test Workflow CRAM_QC_MOSDEPTH_SAMTOOLS"
+    script "../main.nf"
+    workflow "CRAM_QC_MOSDEPTH_SAMTOOLS"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "cram_qc_mosdepth_samtools"
+    tag "subworkflows/cram_qc_mosdepth_samtools"
+    tag "samtools/stats"
+    tag "mosdepth"
+
+    test("homo_sapiens - cram - without intervals") {
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                input[2] = channel.empty()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.reports[0][0],
+                    workflow.out.reports.collect { file(it[1]).name }.sort()
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - cram - with intervals") {
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                input[2] = channel.of([
+                    [id:'intervals'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.reports[0][0],
+                    workflow.out.reports.collect { file(it[1]).name }.sort()
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - cram - stub") {
+
+        options "-stub-run"
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                input[2] = channel.empty()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.reports.collect { file(it[1]).name }
+                ).match() }
+            )
+        }
+    }
+
+}                                      

subworkflows/nf-core/cram_qc_mosdepth_samtools/tests/main.nf.test.snap

@@ -0,0 +1,51 @@
+{
+    "homo_sapiens - cram - stub": {
+        "content": [
+            [
+                "test.global.dist.txt",
+                "test.region.dist.txt",
+                "test.stats"
+            ]
+        ],
+        "timestamp": "2026-06-23T15:00:19.878645",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - cram - with intervals": {
+        "content": [
+            {
+                "id": "test",
+                "single_end": false
+            },
+            [
+                "test.mosdepth.global.dist.txt",
+                "test.mosdepth.region.dist.txt",
+                "test.stats"
+            ]
+        ],
+        "timestamp": "2026-06-23T14:53:34.149357",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - cram - without intervals": {
+        "content": [
+            {
+                "id": "test",
+                "single_end": false
+            },
+            [
+                "test.mosdepth.global.dist.txt",
+                "test.stats"
+            ]
+        ],
+        "timestamp": "2026-06-23T14:53:08.874632",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}