Added delly/filter, changed delly/call - this time with up-to-date fork

modules/nf-core/delly/call/environment.yml

@@ -1,7 +1,9 @@
-name: delly_call
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "delly_call"
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::delly=1.1.6
+  - "bioconda::delly=1.2.6"

modules/nf-core/delly/call/main.nf

@@ -1,35 +1,37 @@
 process DELLY_CALL {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/delly:1.1.6--ha41ced6_0' :
-        'biocontainers/delly:1.1.6--ha41ced6_0' }"
+        'https://depot.galaxyproject.org/singularity/delly:1.2.6--hb7e2ac5_0':
+        'biocontainers/delly:1.2.6--hb7e2ac5_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(vcf), path(vcf_index), path(exclude_bed)
-    path fasta
-    path fai
+    tuple val(meta), path(input_1), path(input_1_idx), path(input_ctrl), path(input_ctrl_idx), path(exclude_bed)
+    tuple val(ref_meta), path(fasta), path(fai)
+    tuple val(vcf_meta), path(vcf), path(vcf_index)
 
     output:
-    tuple val(meta), path("*.{bcf,vcf.gz}")  , emit: bcf
-    tuple val(meta), path("*.{csi,tbi}")     , emit: csi
-    path "versions.yml"                      , emit: versions
+    tuple val(meta), path("*.{bcf,vcf.gz}"), emit: bcf
+    tuple val(meta), path("*.{csi,tbi}")   , emit: csi
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "bcf"
 
+    def input = input_ctrl ? "${input_1} ${input_ctrl}" : "${input_1}"
     def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
 
     def bcf_output = suffix == "bcf" ? "--outfile ${prefix}.bcf" : ""
-    def vcf_output = suffix == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${prefix}.vcf.gz" : ""
+    def vcf_output = suffix == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${args3} ${prefix}.vcf.gz" : ""
 
     def genotype = vcf ? "--vcffile ${vcf}" : ""
 

modules/nf-core/delly/call/meta.yml

@@ -12,32 +12,54 @@ tools:
       documentation: https://github.com/dellytools/delly/blob/master/README.md
       doi: "10.1093/bioinformatics/bts378"
       licence: ["BSD-3-Clause"]
+      args_id: "$args"
+  - bgzip:
+      description: Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: http://www.htslib.org/doc/bgzip.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      args_id: "$args2"
+  - tabix:
+      description: Generic indexer for TAB-delimited genome position files.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: https://www.htslib.org/doc/tabix.1.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+      args_id: "$args3"
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - input:
+  - input_1:
       type: file
       description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
       pattern: "*.{bam,cram}"
-  - input_index:
+  - input_1_idx:
       type: file
       description: Index of the BAM/CRAM file
       pattern: "*.{bai,crai}"
-  - vcf:
+  - input_ctrl:
       type: file
-      description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
-      pattern: "*.{vcf.gz,bcf}"
-  - vcf_index:
+      description: |
+        Optional BAM/CRAM file of matched control sample for somatic variant calling.
+        Must be sorted, indexed, and duplicate marked.
+      pattern: "*.{bam,cram}"
+  - input_ctrl_idx:
       type: file
-      description: The index of the BCF/VCF file
-      pattern: "*.{tbi,csi}"
+      description: Optional index of the control BAM/CRAM file
+      pattern: "*.{bai,crai}"
   - exclude_bed:
       type: file
       description: An optional bed file containing regions to exclude from the called VCF
       pattern: "*.bed"
+  - ref_meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: The reference fasta file
@@ -46,6 +68,19 @@ input:
       type: file
       description: Index of reference fasta file to identify split-reads
       pattern: "*.fai"
+  - vcf_meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
+      pattern: "*.{vcf.gz,bcf}"
+  - vcf_index:
+      type: file
+      description: The index of the BCF/VCF file
+      pattern: "*.{tbi,csi}"
 output:
   - meta:
       type: map
@@ -67,6 +102,8 @@ output:
 authors:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"
 maintainers:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"

modules/nf-core/delly/call/tests/main.nf.test

@@ -0,0 +1,208 @@
+nextflow_process {
+
+    name "Test Process DELLY_CALL"
+    script "../main.nf"
+    process "DELLY_CALL"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "delly"
+    tag "delly/call"
+
+    test("germline - bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("germline - vcf") {
+        when {
+            params {
+                suffix = 'vcf'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("germline - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [],
+                    [],
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                input[2] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+
+    }
+
+    test("somatic - bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'tumor_control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("somatic - vcf") {
+        when {
+            params {
+                suffix = 'vcf'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'tumor_control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [:],
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+}