From 0a8915ae77788a7202b1558ea957650b4f3f9cb8 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Mon, 1 Feb 2021 10:07:35 +0100
Subject: [PATCH] Adding bcftools_tabix module

---
 software/bcftools/tabix/functions.nf | 60 ++++++++++++++++++++++++++
 software/bcftools/tabix/main.nf      | 33 +++++++++++++++
 software/bcftools/tabix/meta.yml     | 63 ++++++++++++++++++++++++++++
 3 files changed, 156 insertions(+)
 create mode 100644 software/bcftools/tabix/functions.nf
 create mode 100644 software/bcftools/tabix/main.nf
 create mode 100644 software/bcftools/tabix/meta.yml

diff --git a/software/bcftools/tabix/functions.nf b/software/bcftools/tabix/functions.nf
new file mode 100644
index 00000000..6f3b4b29
--- /dev/null
+++ b/software/bcftools/tabix/functions.nf
@@ -0,0 +1,60 @@
+
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/software/bcftools/tabix/main.nf b/software/bcftools/tabix/main.nf
new file mode 100644
index 00000000..3e5bba50
--- /dev/null
+++ b/software/bcftools/tabix/main.nf
@@ -0,0 +1,33 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BCFTOOLS_TABIX {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.tbi"), emit: tbi
+    path  "*.version.txt"         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    tabix $options.args $vcf
+    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    """
+}
diff --git a/software/bcftools/tabix/meta.yml b/software/bcftools/tabix/meta.yml
new file mode 100644
index 00000000..51cd0749
--- /dev/null
+++ b/software/bcftools/tabix/meta.yml
@@ -0,0 +1,63 @@
+name: bcftools_tabix
+description: Index GFF/BED/SAM/VCF file
+keywords:
+    - index
+    - vcf
+    - bed
+    - sam
+    - gff
+tools:
+    - stats:
+        description: |
+          Indexes a TAB-delimited genome position file.
+        homepage: http://samtools.github.io/bcftools/bcftools.html
+        documentation: http://www.htslib.org/doc/bcftools.html
+        doi: 10.1093/bioinformatics/btp352
+params:
+    - outdir:
+        type: string
+        description: |
+          The pipeline's output directory. By default, the module will
+          output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+          Value for the Nextflow `publishDir` mode parameter.
+          Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+          Run the module with Conda using the software specified
+          via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+          Instead of directly downloading Singularity images for use with Singularity,
+          force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF input file
+        pattern: "*.{vcf,bed,sam,gff}"
+output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - tbi:
+        type: file
+        description:  Index file
+        pattern: "*.{tbi}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"