From 98c8f44130623e0e53c5a5f3a6435e9544576882 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Wed, 15 Jul 2020 18:15:49 +0200
Subject: [PATCH] Bedtools intersect adapted to the current module standard

---
 software/bedtools/intersect/main.nf               | 13 +++++++++++++
 software/bedtools/intersect/test/input_data/A.bed |  6 +-----
 software/bedtools/intersect/test/input_data/B.bed |  2 +-
 software/bedtools/intersect/test/main.nf          |  4 +++-
 software/bedtools/intersect/test/nextflow.config  |  2 --
 5 files changed, 18 insertions(+), 9 deletions(-)
 mode change 100644 => 120000 software/bedtools/intersect/test/input_data/A.bed
 mode change 100644 => 120000 software/bedtools/intersect/test/input_data/B.bed
 delete mode 100644 software/bedtools/intersect/test/nextflow.config

diff --git a/software/bedtools/intersect/main.nf b/software/bedtools/intersect/main.nf
index a5d3a944..8a5ba53b 100644
--- a/software/bedtools/intersect/main.nf
+++ b/software/bedtools/intersect/main.nf
@@ -1,8 +1,21 @@
+def MODULE = "bedtools_intersect"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
 process INTERSECT_BED {
     tag "$input_file_1-$input_file_2"
 
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    //container "docker.pkg.github.com/nf-core/$MODULE"
     container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
 
+    conda "${moduleDir}/environment.yml"
+
     input:
     path (input_file_1)
     path (input_file_2)
diff --git a/software/bedtools/intersect/test/input_data/A.bed b/software/bedtools/intersect/test/input_data/A.bed
deleted file mode 100644
index dc9a4f0c..00000000
--- a/software/bedtools/intersect/test/input_data/A.bed
+++ /dev/null
@@ -1,5 +0,0 @@
-chr1	951	1061
-chr1	1300	1420
-chr1	1400	1500
-
-
diff --git a/software/bedtools/intersect/test/input_data/A.bed b/software/bedtools/intersect/test/input_data/A.bed
new file mode 120000
index 00000000..4698611f
--- /dev/null
+++ b/software/bedtools/intersect/test/input_data/A.bed
@@ -0,0 +1 @@
+../../../../../tests/data/bed/A.bed
\ No newline at end of file
diff --git a/software/bedtools/intersect/test/input_data/B.bed b/software/bedtools/intersect/test/input_data/B.bed
deleted file mode 100644
index 74e0ef4e..00000000
--- a/software/bedtools/intersect/test/input_data/B.bed
+++ /dev/null
@@ -1 +0,0 @@
-chr1	999	1010
diff --git a/software/bedtools/intersect/test/input_data/B.bed b/software/bedtools/intersect/test/input_data/B.bed
new file mode 120000
index 00000000..d0ad47f4
--- /dev/null
+++ b/software/bedtools/intersect/test/input_data/B.bed
@@ -0,0 +1 @@
+../../../../../tests/data/bed/B.bed
\ No newline at end of file
diff --git a/software/bedtools/intersect/test/main.nf b/software/bedtools/intersect/test/main.nf
index e966ea7a..cb8e7c3d 100644
--- a/software/bedtools/intersect/test/main.nf
+++ b/software/bedtools/intersect/test/main.nf
@@ -2,6 +2,9 @@
 
 nextflow.preview.dsl = 2
 
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
 params.intersect_args = '' //'-bed -c -f 0.20'
 
 include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
@@ -14,5 +17,4 @@ 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/intersect/test/nextflow.config b/software/bedtools/intersect/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/software/bedtools/intersect/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'