Changed nucmer to snippy for assembled genomes

conf/modules.config

@@ -597,7 +597,7 @@ process {
             ]
     }
 
-    withName: SNIPPY_RUN {
+    withName: SNIPPY_RUN_READS {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/VARIANTS/SNIPPY" },
             mode: params.publish_dir_mode,
@@ -610,6 +610,19 @@ process {
         ext.prefix = { "${meta.id}_${meta.mode}" }
     }
 
+    withName: SNIPPY_RUN_CONTIGS {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}/VARIANTS/SNIPPY" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                return filename.replaceAll('^.+/', '')
+            }
+        ]
+        ext.args = { "--mincov ${params.snp_mincov} --minqual ${params.snp_minqual}"
+        }
+        ext.prefix = { "${meta.id}_${meta.mode}" }
+    }   
+
     withName: IGVREPORTS_VCF {
         publishDir = [
             path: { "${params.outdir}/AGGREGATE/VARIANTS/IGVREPORTS" },

modules/local/snippy/run/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::snippy=4.6.0

modules/local/snippy/run/main.nf

@@ -0,0 +1,56 @@
+process SNIPPY_RUN_CONTIGS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' :
+        'biocontainers/snippy:4.6.0--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(contigs)
+    path reference
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.tab")              , emit: tab
+    tuple val(meta), path("${prefix}/${prefix}.csv")              , emit: csv
+    tuple val(meta), path("${prefix}/${prefix}.html")             , emit: html
+    tuple val(meta), path("${prefix}/${prefix}.vcf")              , emit: vcf
+    tuple val(meta), path("${prefix}/${prefix}.bed")              , emit: bed
+    tuple val(meta), path("${prefix}/${prefix}.gff")              , emit: gff
+    tuple val(meta), path("${prefix}/${prefix}.bam")              , emit: bam
+    tuple val(meta), path("${prefix}/${prefix}.bam.bai")          , emit: bai
+    tuple val(meta), path("${prefix}/${prefix}.log")              , emit: log
+    tuple val(meta), path("${prefix}/${prefix}.aligned.fa")       , emit: aligned_fa
+    tuple val(meta), path("${prefix}/${prefix}.consensus.fa")     , emit: consensus_fa
+    tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa
+    tuple val(meta), path("${prefix}/${prefix}.raw.vcf")          , emit: raw_vcf
+    tuple val(meta), path("${prefix}/${prefix}.filt.vcf")         , emit: filt_vcf
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz")           , emit: vcf_gz
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi")       , emit: vcf_csi
+    tuple val(meta), path("${prefix}/${prefix}.txt")              , emit: txt
+    path "versions.yml"                                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    snippy \\
+        $args \\
+        --cpus $task.cpus \\
+        --ram $task.memory \\
+        --outdir $prefix \\
+        --reference $reference \\
+        --prefix $prefix \\
+        --ctgs $contigs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //')
+    END_VERSIONS
+    """
+}

modules/local/snippy/run/meta.yml

@@ -0,0 +1,213 @@
+name: snippy_run
+description: Rapid haploid variant calling
+keywords:
+  - variant
+  - fastq
+  - bacteria
+tools:
+  - snippy:
+      description: "Rapid bacterial SNP calling and core genome alignments"
+      homepage: "https://github.com/tseemann/snippy"
+      documentation: "https://github.com/tseemann/snippy"
+      tool_dev_url: "https://github.com/tseemann/snippy"
+      licence: ["GPL v2"]
+      identifier: biotools:snippy
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+        pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - - reference:
+        type: file
+        description: Reference genome in FASTA format
+        pattern: "*.{fasta,fna,fa}"
+output:
+  - tab:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.tab:
+          type: file
+          description: A simple tab-separated summary of all the variants
+          pattern: "*.tab"
+  - csv:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.csv:
+          type: file
+          description: A comma-separated version of the .tab file
+          pattern: "*.csv"
+  - html:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.html:
+          type: file
+          description: A HTML version of the .tab file
+          pattern: "*.html"
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.vcf:
+          type: file
+          description: The final annotated variants in VCF format
+          pattern: "*.vcf"
+  - bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.bed:
+          type: file
+          description: The variants in BED format
+          pattern: "*.bed"
+  - gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.gff:
+          type: file
+          description: The variants in GFF3 format
+          pattern: "*.gff"
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.bam:
+          type: file
+          description: The alignments in BAM format. Includes unmapped, multimapping reads.
+            Excludes duplicates.
+          pattern: "*.bam"
+  - bai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.bam.bai:
+          type: file
+          description: Index for the .bam file
+          pattern: "*.bam.bai"
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.log:
+          type: file
+          description: A log file with the commands run and their outputs
+          pattern: "*.log"
+  - aligned_fa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.aligned.fa:
+          type: file
+          description: A version of the reference but with - at position with depth=0
+            and N for 0 < depth < --mincov (does not have variants)
+          pattern: "*.aligned.fa"
+  - consensus_fa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.consensus.fa:
+          type: file
+          description: A version of the reference genome with all variants instantiated
+          pattern: "*.consensus.fa"
+  - consensus_subs_fa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.consensus.subs.fa:
+          type: file
+          description: A version of the reference genome with only substitution variants
+            instantiated
+          pattern: "*.consensus.subs.fa"
+  - raw_vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.raw.vcf:
+          type: file
+          description: The unfiltered variant calls from Freebayes
+          pattern: "*.raw.vcf"
+  - filt_vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.filt.vcf:
+          type: file
+          description: The filtered variant calls from Freebayes
+          pattern: "*.filt.vcf"
+  - vcf_gz:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.vcf.gz:
+          type: file
+          description: Compressed .vcf file via BGZIP
+          pattern: "*.vcf.gz"
+  - vcf_csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.vcf.gz.csi:
+          type: file
+          description: Index for the .vcf.gz via bcftools index
+          pattern: "*.vcf.gz.csi"
+  - txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/${prefix}.txt:
+          type: file
+          description: Tab-separated columnar list of statistics
+          pattern: "*.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@rpetit3"
+maintainers:
+  - "@rpetit3"

modules/local/snippy/run/tests/main.nf.test

@@ -0,0 +1,59 @@
+
+nextflow_process {
+
+    name "Test Process SNIPPY_RUN"
+    script "../main.nf"
+    process "SNIPPY_RUN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "snippy"
+    tag "snippy/run"
+
+    test("test-snippy-run") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.tab,
+					process.out.csv,
+					process.out.html,
+					path(process.out.vcf[0][1]).vcf.summary,
+					file(process.out.bed[0][1]).name, // empty: d41d8cd98f00b204e9800998ecf8427e
+					process.out.gff,
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					file(process.out.bai[0][1]).name,
+					file(process.out.log[0][1]).name,
+					process.out.aligned_fa,
+					process.out.consensus_fa,
+					process.out.consensus_subs_fa,
+					path(process.out.raw_vcf[0][1]).vcf.summary,
+					path(process.out.filt_vcf[0][1]).vcf.summary,
+					path(process.out.vcf_gz[0][1]).vcf.summary,
+					file(process.out.vcf_csi[0][1]).name,
+					file(process.out.txt[0][1]).readLines()[3..5],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}