From 99a8196776c5ec958357d34c0c89bf44625bfdf8 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 14 Jul 2020 17:20:12 +0200
Subject: [PATCH] Module bedtools-sort added

---
 software/bedtools/sort/environment.yml       |  9 +++++++
 software/bedtools/sort/main.nf               | 17 +++++++++++++
 software/bedtools/sort/meta.yml              | 26 ++++++++++++++++++++
 software/bedtools/sort/test/input_data/A.bed |  5 ++++
 software/bedtools/sort/test/main.nf          | 17 +++++++++++++
 software/bedtools/sort/test/nextflow.config  |  2 ++
 6 files changed, 76 insertions(+)
 create mode 100644 software/bedtools/sort/environment.yml
 create mode 100644 software/bedtools/sort/main.nf
 create mode 100644 software/bedtools/sort/meta.yml
 create mode 100644 software/bedtools/sort/test/input_data/A.bed
 create mode 100644 software/bedtools/sort/test/main.nf
 create mode 100644 software/bedtools/sort/test/nextflow.config

diff --git a/software/bedtools/sort/environment.yml b/software/bedtools/sort/environment.yml
new file mode 100644
index 00000000..305a5b8f
--- /dev/null
+++ b/software/bedtools/sort/environment.yml
@@ -0,0 +1,9 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-bedtools-sort
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bedtools=2.29.2
diff --git a/software/bedtools/sort/main.nf b/software/bedtools/sort/main.nf
new file mode 100644
index 00000000..1696b458
--- /dev/null
+++ b/software/bedtools/sort/main.nf
@@ -0,0 +1,17 @@
+process BEDTOOLS_SORT {
+    tag { input_file }
+
+    container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
+
+    input:
+    path (input_file)
+    val (bedtools_sort_args)
+
+    output:
+    stdout()
+
+    script:
+    """
+    bedtools sort -i ${input_file} ${bedtools_sort_args}
+    """
+}
diff --git a/software/bedtools/sort/meta.yml b/software/bedtools/sort/meta.yml
new file mode 100644
index 00000000..8452dd2f
--- /dev/null
+++ b/software/bedtools/sort/meta.yml
@@ -0,0 +1,26 @@
+name: bedtools-sort
+description: Returns a sorted feature file by chromosome and other criteria
+keywords:
+    - sort
+tools:
+    - bedtools:
+        description: |
+          Bedtools is a software package that provides with a toolset to perform genome arithmetic operations.
+        homepage: https://bedtools.readthedocs.io/en/latest/index.html
+        documentation: https://bedtools.readthedocs.io/en/latest/index.html
+        doi: 10.093/bioinformatics/btq033
+input:
+    -
+        - input_file:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bed,gff,vcf}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,gff,vcf}"
+authors:
+    - "@JoseEspinosa"
diff --git a/software/bedtools/sort/test/input_data/A.bed b/software/bedtools/sort/test/input_data/A.bed
new file mode 100644
index 00000000..dc9a4f0c
--- /dev/null
+++ b/software/bedtools/sort/test/input_data/A.bed
@@ -0,0 +1,5 @@
+chr1	951	1061
+chr1	1300	1420
+chr1	1400	1500
+
+
diff --git a/software/bedtools/sort/test/main.nf b/software/bedtools/sort/test/main.nf
new file mode 100644
index 00000000..bbf445e3
--- /dev/null
+++ b/software/bedtools/sort/test/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.bedtools_sort_args = '' //'-sizeD'
+
+include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
+include BEDTOOLS_SORT from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('./input_data/A.bed')
+
+// Run the workflow
+workflow {
+    BEDTOOLS_SORT(ch_input, params.bedtools_sort_args)
+    // .check_output()
+}
diff --git a/software/bedtools/sort/test/nextflow.config b/software/bedtools/sort/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/software/bedtools/sort/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'