Add Atlas/PMD (#1810)

* add atlas/pmd
* update atlas/pmd tests
* Add atlas/PMD module
* Remove comment
* Run Prettier
* Incorporate Review by @jfy133

Co-authored-by: maxibor <maxime.borry@gmail.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/atlas/pmd/main.nf

@@ -0,0 +1,42 @@
+process ATLAS_PMD {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
+        'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(pool_rg_txt)
+    path(fasta)
+    path(fai)
+
+    output:
+    tuple val(meta), path("*_PMD_input_Empiric.txt")    , emit: empiric
+    tuple val(meta), path("*_PMD_input_Exponential.txt"), emit: exponential
+    tuple val(meta), path("*_PMD_Table_counts.txt")     , emit: counts
+    tuple val(meta), path("*_PMD_Table.txt")            , emit: table
+    path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def pool_rg_txt = pool_rg_txt ? "poolReadGroups=${pool_rg_txt}" : ""
+    """
+    atlas \\
+        $pool_rg_txt \\
+        task=PMD \\
+        bam=${bam} \\
+        fasta=${fasta} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')
+    END_VERSIONS
+    """
+}

modules/atlas/pmd/meta.yml

@@ -0,0 +1,83 @@
+name: "atlas_pmd"
+description: Estimate the post-mortem damage patterns of DNA
+keywords:
+  - ancient DNA
+  - post mortem damage
+  - bam
+tools:
+  - "atlas":
+      description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
+      homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
+      documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
+      tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
+      doi: "10.1101/105346"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+
+  - bam:
+      type: file
+      description: Single input BAM file
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: The BAI file for the input BAM file
+      pattern: "*.bai"
+  - fasta:
+      type: file
+      description: The reference genome provided as FASTA file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: The FAI file for the reference genome FASTA file
+      pattern: "*.fai"
+  - pool_rg_txt:
+      type: file
+      description: |
+        Optional. Provide the names of read groups that should be merged for PMD estimation.
+        All read groups that should be pooled listed on one line, separated by any white space.
+        Other read groups will be recalibrated separately.
+      pattern: "*.txt"
+
+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"
+
+  - empiric:
+      type: file
+      description: A list of pmd patterns estimated with the empirical method for each readgroup
+      pattern: "*_PMD_input_Empiric.txt"
+  - exponential:
+      type: file
+      description: A list of pmd patterns estimated with the exponential method for each readgroup
+      pattern: "*_PMD_input_Exponential.txt"
+  - counts:
+      type: file
+      description: |
+        The counts of all possible transitions for each read position
+        (or up to a certain position, see specific command length)
+      pattern: "*_PMD_Table_counts.txt"
+  - table:
+      type: file
+      description: |
+        For all possible transitions the ratio of the transition counts,
+        which are taken from the _counts.txt table, over the total amount
+        of the base that was mutated, for each position and readgroup
+      pattern: "*_PMD_Table.txt"
+
+authors:
+  - "@maxibor"
+  - "@merszym"

tests/config/pytest_modules.yml

@@ -86,6 +86,10 @@ ataqv/ataqv:
   - modules/ataqv/ataqv/**
   - tests/modules/ataqv/ataqv/**
 
+atlas/pmd:
+  - modules/atlas/pmd/**
+  - tests/modules/atlas/pmd/**
+
 atlas/splitmerge:
   - modules/atlas/splitmerge/**
   - tests/modules/atlas/splitmerge/**

tests/modules/atlas/pmd/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATLAS_PMD } from '../../../../modules/atlas/pmd/main.nf'
+
+workflow test_atlas_pmd {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        []
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    ATLAS_PMD ( input, fasta, fai )
+}

tests/modules/atlas/pmd/nextflow.config

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

tests/modules/atlas/pmd/test.yml

@@ -0,0 +1,14 @@
+- name: atlas pmd test_atlas_pmd
+  command: nextflow run ./tests/modules/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config  -c ./tests/modules/atlas/pmd/nextflow.config
+  tags:
+    - atlas/pmd
+    - atlas
+  files:
+    - path: output/atlas/test.paired_end.sorted_PMD_Table.txt
+      md5sum: b28a9f4784f30a711046708eb7d94642
+    - path: output/atlas/test.paired_end.sorted_PMD_Table_counts.txt
+      md5sum: 1aabfb83cfff6e0413f52d016c943e3e
+    - path: output/atlas/test.paired_end.sorted_PMD_input_Empiric.txt
+      md5sum: 8ff876f50ce05dc9aac0646a31682df0
+    - path: output/atlas/test.paired_end.sorted_PMD_input_Exponential.txt
+      md5sum: 2421450ef643316f4eacf5cb811e4df7