Somalier relate (#2001)

* Working version of somalier relate

* few changes

* new changes

* corrected test.yml

* updated container paths and file paths

* changed container and inputFile paths

* changed left padding

* requested changes

* Update modules/somalier/relate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/somalier/relate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* requested changes

* requested changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/somalier/relate/main.nf

@@ -0,0 +1,46 @@
+
+process SOMALIER_RELATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0':
+        'quay.io/biocontainers/somalier:0.2.15--h37c5b7d_0' }"
+
+    input:
+    tuple val(meta), path(extract)
+    path(sample_groups)
+    path(ped)
+
+    output:
+    tuple val(meta), path("*.html"),          emit: html
+    tuple val(meta), path("*.pairs.tsv"),     emit: pairs_tsv
+    tuple val(meta), path("*.samples.tsv"),   emit: samples_tsv
+    path "versions.yml",                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def input_list = extract.collect{"$it"}.join(' ')
+    def prefix = task.ext.prefix ?: "$meta.id"
+    def sample_groups_command = sample_groups ? "-g $sample_groups" : ""
+    def ped_command = ped ? "-p $ped" : ""
+
+    """
+    somalier relate \\
+        -o ${prefix} \\
+        ${input_list} \\
+        ${args} \\
+        ${sample_groups_command} \\
+        ${ped_command}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//')
+    END_VERSIONS
+    """
+
+}

modules/somalier/relate/meta.yml

@@ -0,0 +1,62 @@
+name: "somalier_relate"
+description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
+keywords:
+  - relatedness
+  - QC
+  - bam
+  - cram
+  - vcf
+  - gvcf
+  - ancestry
+  - identity
+  - kinship
+  - informative sites
+  - family
+tools:
+  - "somalier":
+      description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
+      homepage: "https://github.com/brentp/somalier"
+      documentation: "https://github.com/brentp/somalier/blob/master/README.md"
+      tool_dev_url: "https://github.com/brentp/somalier"
+      doi: "https://doi.org/10.1186/s13073-020-00761-2"
+      licence: "MIT License"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - extract:
+      type: file
+      description: extract file from Somlaier extract
+      pattern: "*.somalier"
+  - sample_groups:
+      type: file
+      description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
+      pattern: "*.{txt,csv}"
+  - ped:
+      type: file
+      description: optional path to a ped or fam file indicating the expected relationships among samples
+      pattern: "*.{ped,fam}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - html:
+      type: file
+      description: html file
+      pattern: "*.html"
+  - pairs_tsv:
+      type: file
+      description: tsv file with output stats for pairs of samples
+      pattern: "*.pairs.tsv"
+  - samples_tsv:
+      type: file
+      description: tsv file with sample-level information
+      pattern: "*.samples.tsv"
+
+authors:
+  - "@ashotmarg"

tests/config/pytest_modules.yml

@@ -2223,6 +2223,10 @@ somalier/extract:
   - modules/somalier/extract/**
   - tests/modules/somalier/extract/**
 
+somalier/relate:
+  - modules/somalier/relate/**
+  - tests/modules/somalier/relate/**
+
 sourmash/sketch:
   - modules/sourmash/sketch/**
   - tests/modules/sourmash/sketch/**

tests/modules/somalier/relate/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SOMALIER_RELATE } from '../../../../modules/somalier/relate/main.nf'
+
+
+workflow test_somalier_relate {
+
+    input = [ [ id:'cohort', single_end:false ], // meta map
+        [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
+    ]
+
+    SOMALIER_RELATE (input,[],[])
+}
+
+
+workflow test_somalier_relate_ped_groups {
+
+input = [ [ id:'cohort', single_end:false ], // meta map
+    [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
+    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
+]
+
+    groups = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/groups.txt", checkIfExists: true)
+    ped = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/family.ped", checkIfExists: true)
+
+    SOMALIER_RELATE (input,groups,ped)
+}

tests/modules/somalier/relate/nextflow.config

@@ -0,0 +1,9 @@
+params.prefix = ""
+
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:SOMALIER_RELATE {
+        ext.prefix = { params.prefix ? "${params.prefix}." : ""}
+    }
+}

tests/modules/somalier/relate/test.yml

@@ -0,0 +1,25 @@
+- name: somalier relate test_somalier_relate
+  command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate
+  tags:
+    - somalier/relate
+    - somalier
+  files:
+    - path: output/somalier/cohort.html
+      md5sum: 03cac9b2c67a8a06f63e07f83ee11e18
+    - path: output/somalier/cohort.pairs.tsv
+      md5sum: 54d1e9fca1bf9d747d4254c6fa98edcf
+    - path: output/somalier/cohort.samples.tsv
+      md5sum: 97257d88886db1325c4d7d10cefa7169
+
+- name: somalier relate test_somalier_relate_ped_groups
+  command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups
+  tags:
+    - somalier/relate
+    - somalier
+  files:
+    - path: output/somalier/cohort.html
+      md5sum: 0d573016c9279ccdfdcfd4eb01d73b89
+    - path: output/somalier/cohort.pairs.tsv
+      md5sum: 8655714f1e5359329188e9f501168131
+    - path: output/somalier/cohort.samples.tsv
+      md5sum: 38ef93340e55fbeef47640abda9e48b0