updated input, output and test after review

modules/nf-core/topas/gencons/main.nf

@@ -9,20 +9,27 @@ process TOPAS_GENCONS {
 
     input:
     tuple val(meta), path(vcf)
+    tuple val(meta), path(vcf_indels)
     tuple val(meta), path(reference)
+    tuple val(meta), path(fai)
+    val(vcf_output)
 
     output:
     tuple val(meta), path("*.fasta.gz"), emit: fasta
-    tuple val(meta), path("*.ccf")     ,      emit: ccf
-    tuple val(meta), path("*.log")     ,      emit: log
-    path "versions.yml"                ,      emit: versions
+    tuple val(meta), path("*.vcf.gz")  , emit: vcf     , optional: true
+    tuple val(meta), path("*.ccf")     , emit: ccf
+    tuple val(meta), path("*.log")     , emit: log
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def optionalvcfindels = vcf_indels ? "-indels ${vcf_indels}" : ''
+    def optionalfai = fai ? "-fai ${fai}" : ''
+    def vcfoutput = vcf_output ? "-vcf_out ${prefix}.vcf" : ""
     def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
@@ -32,9 +39,15 @@ process TOPAS_GENCONS {
         $args \\
         -o ${prefix}.fasta \\
         -snps $vcf \\
+        $optionalvcfindels \\
+        $vcfoutput \\
         -ref $reference
 
-    gzip ${prefix}.fasta
+    gzip -n ${prefix}.fasta
+
+    if [[ -f ${prefix}.vcf ]];then
+        gzip -n ${prefix}.vcf
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/topas/gencons/meta.yml

@@ -1,5 +1,5 @@
 name: "topas_gencons"
-description: Create fasta consensus with TOPAS toolkit
+description: Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA
 keywords:
   - consensus
   - fasta
@@ -22,14 +22,28 @@ input:
 
   - vcf:
       type: file
-      description: compressed vcf file containing the called snps
+      description: Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps
+      pattern: "*.vcf.gz"
+
+  - vcf_indels:
+      type: file
+      description: Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels
       pattern: "*.vcf.gz"
 
   - reference:
       type: file
       description: Fasta file of reference genome
       pattern: "*.fasta"
 
+  - fai:
+      type: file
+      description: Optional index for the fasta file of reference genome
+      pattern: "*.fai"
+
+  - vcf_output:
+      type: boolean
+      description: Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced
+
 output:
   - meta:
       type: map
@@ -47,6 +61,11 @@ output:
       description: Gzipped consensus fasta file with bases under threshold replaced with Ns
       pattern: "*.fasta.gz"
 
+  - vcf:
+      type: file
+      description: Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns
+      pattern: "*.vcf.gz"
+
   - ccf:
       type: file
       description: Statistics file containing information about the consensus calls in the fasta file

tests/modules/nf-core/topas/gencons/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
+include { GATK_UNIFIEDGENOTYPER as GATK_UNIFIEDGENOTYPERSNPS } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
+include { GATK_UNIFIEDGENOTYPER as GATK_UNIFIEDGENOTYPERINDELS } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
 include { TOPAS_GENCONS         } from '../../../../../modules/nf-core/topas/gencons/main.nf'
 
 workflow test_topas_gencons {
@@ -24,13 +25,78 @@ workflow test_topas_gencons {
         file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
     ]
 
-    GATK_UNIFIEDGENOTYPER ( input_gatk, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
+    GATK_UNIFIEDGENOTYPERSNPS ( input_gatk, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
 
-    gencons_vcf = GATK_UNIFIEDGENOTYPER.out.vcf
+    gencons_vcf = GATK_UNIFIEDGENOTYPERSNPS.out.vcf
+    gencons_vcf_indels = [[],[]]
     gencons_fasta =[ [ id:'test' ], // meta map
                      file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
                     ]
+    gencons_vcf_output = false
 
+    TOPAS_GENCONS ( gencons_vcf, gencons_vcf_indels, gencons_fasta, [[],[]], gencons_vcf_output)
+}
+
+workflow test_topas_gencons_fai {
+
+    input_gatk = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+    fai = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
+    dict = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    ]
+
+    GATK_UNIFIEDGENOTYPERSNPS ( input_gatk, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
+
+    gencons_vcf = GATK_UNIFIEDGENOTYPERSNPS.out.vcf
+    gencons_vcf_indels = [[],[]]
+    gencons_fasta =[ [ id:'test' ], // meta map
+                     file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+    gencons_vcf_output = false
+
+    TOPAS_GENCONS ( gencons_vcf, gencons_vcf_indels, gencons_fasta, fai, gencons_vcf_output)
+}
+
+workflow test_topas_gencons_indels {
+
+    input_gatk = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+    fai = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
+    dict = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    ]
+
+    GATK_UNIFIEDGENOTYPERSNPS ( input_gatk, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
+    GATK_UNIFIEDGENOTYPERINDELS ( input_gatk, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
+
+
+    gencons_vcf = GATK_UNIFIEDGENOTYPERSNPS.out.vcf
+    gencons_vcf_indels = GATK_UNIFIEDGENOTYPERINDELS.out.vcf
+    gencons_fasta =[ [ id:'test' ], // meta map
+                     file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+    gencons_vcf_output = true
 
-    TOPAS_GENCONS ( gencons_vcf, gencons_fasta )
+    TOPAS_GENCONS ( gencons_vcf, gencons_vcf_indels, gencons_fasta, [[],[]], gencons_vcf_output)
 }

tests/modules/nf-core/topas/gencons/nextflow.config

@@ -2,8 +2,14 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: GATK_UNIFIEDGENOTYPER {
+    withName: GATK_UNIFIEDGENOTYPERSNPS {
         ext.args = "--genotype_likelihoods_model SNP -stand_call_conf 30 --sample_ploidy 2 -dcov 250 --output_mode EMIT_ALL_SITES"
+        ext.prefix = { "${meta.id}_snps" }
+    }
+
+    withName: GATK_UNIFIEDGENOTYPERINDELS {
+        ext.args = "--genotype_likelihoods_model INDEL -stand_call_conf 30 --sample_ploidy 2 -dcov 250 --output_mode EMIT_ALL_SITES"
+        ext.prefix = { "${meta.id}_indels" }
     }
 
 }

tests/modules/nf-core/topas/gencons/test.yml

@@ -1,14 +1,46 @@
 - name: topas gencons test_topas_gencons
   command: nextflow run ./tests/modules/nf-core/topas/gencons -entry test_topas_gencons -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/topas/gencons/nextflow.config
+  tags:
+    - topas
+    - topas/gencons
+  files:
+    - path: output/topas/[].fasta.ccf
+      md5sum: 794d4231ee35302a9816df2c1f595041
+    - path: output/topas/[].fasta.gz
+      md5sum: 1f219a39d28eed85be8a48cb167d5879
+    - path: output/topas/[].fasta.log
+      contains:
+        - "Use -? for help"
+    - path: output/topas/versions.yml
+
+- name: topas gencons test_topas_gencons_fai
+  command: nextflow run ./tests/modules/nf-core/topas/gencons -entry test_topas_gencons_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/topas/gencons/nextflow.config
   tags:
     - topas
     - topas/gencons
   files:
     - path: output/topas/test.fasta.ccf
-      md5sum: ed5d5767d014d76d5ba904017d937cd5
+      md5sum: 794d4231ee35302a9816df2c1f595041
     - path: output/topas/test.fasta.gz
       md5sum: 1f219a39d28eed85be8a48cb167d5879
     - path: output/topas/test.fasta.log
       contains:
         - "Use -? for help"
     - path: output/topas/versions.yml
+
+- name: topas gencons test_topas_gencons_indels
+  command: nextflow run ./tests/modules/nf-core/topas/gencons -entry test_topas_gencons_indels -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/topas/gencons/nextflow.config
+  tags:
+    - topas
+    - topas/gencons
+  files:
+    - path: output/topas/[].fasta.ccf
+      md5sum: f7337d6e701ab7c5b3c8654742e5116a
+    - path: output/topas/[].fasta.gz
+      md5sum: 1f219a39d28eed85be8a48cb167d5879
+    - path: output/topas/[].fasta.log
+      contains:
+        - "Use -? for help"
+    - path: output/topas/[].vcf.gz
+      md5sum: 91806432f141a2a7a071283aa962488d
+    - path: output/topas/versions.yml