From 708cee9caed2542e7178653844ca18a24ec53f43 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 14 Jul 2020 16:17:23 +0200
Subject: [PATCH] Module bedtools-intersectbed added

---
 software/bedtools/intersectbed/Dockerfile     |  7 +++++
 .../bedtools/intersectbed/environment.yml     |  9 ++++++
 software/bedtools/intersectbed/main.nf        | 19 ++++++++++++
 software/bedtools/intersectbed/meta.yml       | 30 +++++++++++++++++++
 .../intersectbed/test/input_data/A.bed        |  5 ++++
 .../intersectbed/test/input_data/B.bed        |  1 +
 software/bedtools/intersectbed/test/main.nf   | 18 +++++++++++
 .../intersectbed/test/nextflow.config         |  2 ++
 8 files changed, 91 insertions(+)
 create mode 100644 software/bedtools/intersectbed/Dockerfile
 create mode 100644 software/bedtools/intersectbed/environment.yml
 create mode 100644 software/bedtools/intersectbed/main.nf
 create mode 100644 software/bedtools/intersectbed/meta.yml
 create mode 100644 software/bedtools/intersectbed/test/input_data/A.bed
 create mode 100644 software/bedtools/intersectbed/test/input_data/B.bed
 create mode 100644 software/bedtools/intersectbed/test/main.nf
 create mode 100644 software/bedtools/intersectbed/test/nextflow.config

diff --git a/software/bedtools/intersectbed/Dockerfile b/software/bedtools/intersectbed/Dockerfile
new file mode 100644
index 00000000..94ce0c08
--- /dev/null
+++ b/software/bedtools/intersectbed/Dockerfile
@@ -0,0 +1,7 @@
+FROM nfcore/base
+LABEL authors="Jose Espinosa-Carrasco" \
+    description="Docker image containing all requirements for nf-core/modules/bedtools/intersect"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-bedtools-intersectbed/bin:$PATH
diff --git a/software/bedtools/intersectbed/environment.yml b/software/bedtools/intersectbed/environment.yml
new file mode 100644
index 00000000..eb0a4040
--- /dev/null
+++ b/software/bedtools/intersectbed/environment.yml
@@ -0,0 +1,9 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-bedtools-intersectbed
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bedtools=2.29.2
diff --git a/software/bedtools/intersectbed/main.nf b/software/bedtools/intersectbed/main.nf
new file mode 100644
index 00000000..a5d3a944
--- /dev/null
+++ b/software/bedtools/intersectbed/main.nf
@@ -0,0 +1,19 @@
+process INTERSECT_BED {
+    tag "$input_file_1-$input_file_2"
+
+    container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
+
+    input:
+    path (input_file_1)
+    path (input_file_2)
+    val (intersectbed_args)
+
+    output:
+    stdout()
+
+    script:
+    """
+    bedtools intersect -a ${input_file_1} -b ${input_file_2} ${intersectbed_args}
+    """
+}
+
diff --git a/software/bedtools/intersectbed/meta.yml b/software/bedtools/intersectbed/meta.yml
new file mode 100644
index 00000000..374fd3e7
--- /dev/null
+++ b/software/bedtools/intersectbed/meta.yml
@@ -0,0 +1,30 @@
+name: bedtools intersect
+description: Returns the overlapping features between two sets of genomics features
+keywords:
+    - intersect,bed,bedtools
+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_1:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bam,bed,BED,gff,vcf}"
+        - input_file_2:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bam,bed,BED,gff,vcf}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,BED}"
+authors:
+    - "@JoseEspinosa"
diff --git a/software/bedtools/intersectbed/test/input_data/A.bed b/software/bedtools/intersectbed/test/input_data/A.bed
new file mode 100644
index 00000000..dc9a4f0c
--- /dev/null
+++ b/software/bedtools/intersectbed/test/input_data/A.bed
@@ -0,0 +1,5 @@
+chr1	951	1061
+chr1	1300	1420
+chr1	1400	1500
+
+
diff --git a/software/bedtools/intersectbed/test/input_data/B.bed b/software/bedtools/intersectbed/test/input_data/B.bed
new file mode 100644
index 00000000..74e0ef4e
--- /dev/null
+++ b/software/bedtools/intersectbed/test/input_data/B.bed
@@ -0,0 +1 @@
+chr1	999	1010
diff --git a/software/bedtools/intersectbed/test/main.nf b/software/bedtools/intersectbed/test/main.nf
new file mode 100644
index 00000000..e966ea7a
--- /dev/null
+++ b/software/bedtools/intersectbed/test/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.intersect_args = '' //'-bed -c -f 0.20'
+
+include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
+include INTERSECT_BED from '../main.nf' params(params)
+
+// Define input channels
+ch_input_1 = Channel.fromPath('./input_data/A.bed')
+ch_input_2 = Channel.fromPath('./input_data/B.bed')
+
+// Run the workflow
+workflow {
+    INTERSECT_BED(ch_input_1, ch_input_2, params.intersect_args)
+    // .check_output()
+}
diff --git a/software/bedtools/intersectbed/test/nextflow.config b/software/bedtools/intersectbed/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/software/bedtools/intersectbed/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'