Picard liftover vcf (#1431)

* Building Picard liftovervcf module

* Building Picard liftovervcf module_test

* Building Picard liftovervcf pytest

* Module for picard liftover vcf created

* Fixed files after linting test

* Fixed trailing whitespace

* Checked files with prettier

* further formatting with prettier

* Fixed test.yml

* Fixed input variable names

* Changed contain test.liftef.vcf

* Changed contain in test.yml test.liftef.vcf

* Run prittier

* Going back to previous version of test.yml

* downgrading picard to 2.26.10 from 2.26.11

* Update modules/picard/liftovervcf/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/main.nf

Print available memory

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Output from .vcf to .vcf.gz

* Added spaces to align emit

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Removing md5sum test

Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

modules/picard/liftovervcf/main.nf

@@ -0,0 +1,49 @@
+process PICARD_LIFTOVERVCF {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input_vcf)
+    path dict
+    path chain
+    path fasta
+
+    output:
+    tuple val(meta), path("*lifted.vcf.gz")  , emit: vcf_lifted
+    tuple val(meta), path("*unlifted.vcf.gz"), emit: vcf_unlifted
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 1
+    if (!task.memory) {
+        log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        LiftoverVcf \\
+        $args \\
+        I=$input_vcf \\
+        O=${prefix}.lifted.vcf.gz \\
+        CHAIN=$chain \\
+        REJECT=${prefix}.unlifted.vcf.gz \\
+        R=$fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/liftovervcf/meta.yml

@@ -0,0 +1,55 @@
+name: picard_liftovervcf
+description: convert between genome builds
+keywords:
+  - liftOver
+  - picard
+tools:
+  - picard:
+      description: Move annotations from one assembly to another
+      homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
+      tool_dev_url: https://github.com/broadinstitute/picard
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input_vcf:
+      type: file
+      description: VCF file
+      pattern: "*.{vcf,vcf.gz}"
+  - chain:
+      type: file
+      description: The liftover chain file
+  - fasta:
+      type: file
+      description: fasta file
+      pattern: "*.fasta"
+  - dict:
+      type: file
+      description: dictionary for fasta file
+      pattern: "*.{dict}"
+
+output:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf_lifted:
+      type: file
+      description: VCF file containing successfully lifted variants
+      pattern: "*.{lifted.vcf.gz}"
+  - vcf_unlifted:
+      type: file
+      description: VCF file containing unsuccessfully lifted variants
+      pattern: "*.{unlifted.vcf.gz}"
+
+authors:
+  - "@lucpen"

tests/config/pytest_modules.yml

@@ -1351,6 +1351,10 @@ picard/fixmateinformation:
   - modules/picard/fixmateinformation/**
   - tests/modules/picard/fixmateinformation/**
 
+picard/liftovervcf:
+  - modules/picard/liftovervcf/**
+  - tests/modules/picard/liftovervcf/**
+
 picard/markduplicates:
   - modules/picard/markduplicates/**
   - tests/modules/picard/markduplicates/**

tests/modules/picard/liftovervcf/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf'
+
+workflow test_picard_liftovervcf {
+
+    input_vcf = [ [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+            ]
+    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
+}

tests/modules/picard/liftovervcf/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    ext.args = "WARN_ON_MISSING_CONTIG=true"
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/picard/liftovervcf/test.yml

@@ -0,0 +1,11 @@
+- name: picard liftovervcf test_picard_liftovervcf
+  command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config
+  tags:
+    - picard/liftovervcf
+    - picard
+  files:
+    - path: output/picard/test.lifted.vcf.gz
+      contains:
+        - "chr22"
+    - path: output/picard/test.unlifted.vcf.gz
+    - path: output/picard/versions.yml