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

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:1.2.6--hb7e2ac5_1' :
         'biocontainers/delly:1.2.6--hb7e2ac5_1' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(vcf), path(vcf_index), path(exclude_bed)
+    tuple val(meta), path(input_1), path(input_1_idx), path(input_ctrl), path(input_ctrl_idx), path(vcf), path(vcf_index), path(exclude_bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
     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

@@ -12,20 +12,45 @@ 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}"
+  - input_ctrl:
+      type: file
+      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: Optional index of the control BAM/CRAM file
+      pattern: "*.{bai,crai}"
   - vcf:
       type: file
       description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
@@ -77,6 +102,8 @@ output:
 authors:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"
 maintainers:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"