From 8c3d7aa2d8f5267993a822ec31de85575b0e0bbe Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 14 Jul 2020 17:25:32 +0200
Subject: [PATCH] Standardizing process names to BEDTOOLS_FOO and same with
 some variables

---
 software/bedtools/complementbed/environment.yml |  2 +-
 software/bedtools/complementbed/main.nf         | 12 ++++++------
 software/bedtools/complementbed/test/main.nf    |  6 +++---
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/software/bedtools/complementbed/environment.yml b/software/bedtools/complementbed/environment.yml
index cb03d5e4..544f0e6e 100644
--- a/software/bedtools/complementbed/environment.yml
+++ b/software/bedtools/complementbed/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-bedtools-complementbed
+name: nf-core-bedtools-complement
 channels:
   - conda-forge
   - bioconda
diff --git a/software/bedtools/complementbed/main.nf b/software/bedtools/complementbed/main.nf
index d22ce418..7c34ba8f 100644
--- a/software/bedtools/complementbed/main.nf
+++ b/software/bedtools/complementbed/main.nf
@@ -1,18 +1,18 @@
-process COMPLEMENT_BED {
+process BEDTOOLS_COMPLEMENT {
     tag {input_file}
 
     container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
 
     input:
-        path (input_file)
-        path (fasta_sizes)
-        val (complementbed_args)
+    path (input_file)
+    path (fasta_sizes)
+    val (bedtools_complement_args)
 
     output:
-        stdout()
+    stdout()
 
     script:
     """
-    bedtools complement -i ${input_file} -g ${fasta_sizes} ${complementbed_args}
+    bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args}
     """
 }
diff --git a/software/bedtools/complementbed/test/main.nf b/software/bedtools/complementbed/test/main.nf
index 9efe59f6..e5722133 100644
--- a/software/bedtools/complementbed/test/main.nf
+++ b/software/bedtools/complementbed/test/main.nf
@@ -2,10 +2,10 @@
 
 nextflow.preview.dsl = 2
 
-params.complementbed_args = ''
+params.bedtools_complement_args = ''
 
 include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
-include COMPLEMENT_BED from '../main.nf' params(params)
+include BEDTOOLS_COMPLEMENT from '../main.nf' params(params)
 
 // Define input channels
 ch_input = Channel.fromPath('./input_data/A.bed')
@@ -13,6 +13,6 @@ chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
 
 // Run the workflow
 workflow {
-    COMPLEMENT_BED(ch_input, chrom_sizes, params.complementbed_args)
+    BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args)
     // .check_output()
 }