Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0

modules/sexdeterrmine/main.nf

@@ -0,0 +1,40 @@
+process SEXDETERRMINE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
+        'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(depth)
+    path sample_list_file
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.tsv") , emit: tsv
+    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 sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
+    if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    sexdeterrmine \\
+        -I $depth \\
+        $sample_list \\
+        $args \\
+        > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
+    END_VERSIONS
+    """
+}

modules/sexdeterrmine/meta.yml

@@ -0,0 +1,48 @@
+name: "sexdeterrmine"
+description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
+keywords:
+  - sex determination
+  - genetic sex
+  - relative coverage
+  - ancient dna
+tools:
+  - "sexdeterrmine":
+      description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
+      homepage: "https://github.com/TCLamnidis/Sex.DetERRmine"
+      documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
+      tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
+      doi: "https://doi.org/10.1038/s41467-018-07483-5"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - depth:
+      type: file
+      description: Output from samtools depth (with header)
+      pattern: "*"
+
+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"
+  - json:
+      type: file
+      description: JSON formatted table of relative coverages on the X and Y, with associated error bars.
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: TSV table of relative coverages on the X and Y, with associated error bars.
+      pattern: "*.tsv"
+
+authors:
+  - "@TCLamnidis"

tests/config/pytest_modules.yml

@@ -1851,6 +1851,10 @@ seqwish/induce:
   - modules/seqwish/induce/**
   - tests/modules/seqwish/induce/**
 
+sexdeterrmine:
+  - modules/sexdeterrmine/**
+  - tests/modules/sexdeterrmine/**
+
 shasum:
   - modules/shasum/**
   - tests/modules/shasum/**

tests/config/test_data.config

@@ -232,10 +232,11 @@ params {
                 test2_paired_end_umi_unsorted_bam              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
                 test2_paired_end_umi_unsorted_tagged_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
 
-
                 mitochon_standin_recalibrated_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
                 mitochon_standin_recalibrated_sorted_bam_bai   = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
 
+                test3_single_end_markduplicates_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
+
                 test_paired_end_sorted_cram                      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
                 test_paired_end_sorted_cram_crai                 = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
                 test_paired_end_markduplicates_sorted_cram       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"

tests/modules/sexdeterrmine/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf'
+include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf'
+
+workflow test_sexdeterrmine {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
+
+    SAMTOOLS_DEPTH ( input )
+    SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
+}

tests/modules/sexdeterrmine/nextflow.config

@@ -0,0 +1,12 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:SAMTOOLS_DEPTH {
+        ext.args = "-H"
+    }
+
+    withName:SEXDETERRMINE {
+        ext.prefix = { "${meta.id}_sexdet" }
+    }
+}

tests/modules/sexdeterrmine/test.yml

@@ -0,0 +1,15 @@
+- name: sexdeterrmine test_sexdeterrmine
+  command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
+  tags:
+    - sexdeterrmine
+  files:
+    - path: output/samtools/test.tsv
+      md5sum: fa2992ca1ea93a6e1b3e838476191935
+    - path: output/samtools/versions.yml
+      md5sum: dbd04b700335c8ad236bd667254c8dd8
+    - path: output/sexdeterrmine/sexdeterrmine.json
+      md5sum: bafb2419bb8630eda29a251c20e97166
+    - path: output/sexdeterrmine/test_sexdet.tsv
+      md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
+    - path: output/sexdeterrmine/versions.yml
+      md5sum: 077361101e8e7997aec3da8a01e59eee