From 2cbc988d5f7d8b0fc37a7b8a3a49f795396f982a Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Wed, 15 Jul 2020 18:15:16 +0200
Subject: [PATCH] Bedtools complement adapted to the current module standard

---
 software/bedtools/complement/Dockerfile       |  4 ++--
 software/bedtools/complement/main.nf          | 19 +++++++++++++++++--
 .../bedtools/complement/test/input_data/A.bed |  6 +-----
 .../complement/test/input_data/genome.sizes   |  2 +-
 software/bedtools/complement/test/main.nf     |  5 +++--
 .../bedtools/complement/test/nextflow.config  |  2 --
 6 files changed, 24 insertions(+), 14 deletions(-)
 mode change 100644 => 120000 software/bedtools/complement/test/input_data/A.bed
 mode change 100644 => 120000 software/bedtools/complement/test/input_data/genome.sizes
 delete mode 100644 software/bedtools/complement/test/nextflow.config

diff --git a/software/bedtools/complement/Dockerfile b/software/bedtools/complement/Dockerfile
index 7eaea60c..1d9dbb95 100644
--- a/software/bedtools/complement/Dockerfile
+++ b/software/bedtools/complement/Dockerfile
@@ -1,7 +1,7 @@
 FROM nfcore/base
 LABEL authors="Jose Espinosa-Carrasco" \
-    description="Docker image containing all requirements for nf-core/modules/bedtools/complementbed"
+    description="Docker image containing all requirements for nf-core/modules/bedtools/complement"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-bedtools-complementbed/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-bedtools-complement/bin:$PATH
diff --git a/software/bedtools/complement/main.nf b/software/bedtools/complement/main.nf
index 7c34ba8f..8e99e58b 100644
--- a/software/bedtools/complement/main.nf
+++ b/software/bedtools/complement/main.nf
@@ -1,18 +1,33 @@
+def MODULE = "bedtools_complement"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
 process BEDTOOLS_COMPLEMENT {
     tag {input_file}
 
+    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)
     path (fasta_sizes)
     val (bedtools_complement_args)
 
     output:
-    stdout()
+    path "${input_file}.bed", emit: complement
+    path "*.version.txt", emit: version
 
     script:
     """
-    bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args}
+    bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args} > ${input_file}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }
diff --git a/software/bedtools/complement/test/input_data/A.bed b/software/bedtools/complement/test/input_data/A.bed
deleted file mode 100644
index dc9a4f0c..00000000
--- a/software/bedtools/complement/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/complement/test/input_data/A.bed b/software/bedtools/complement/test/input_data/A.bed
new file mode 120000
index 00000000..4698611f
--- /dev/null
+++ b/software/bedtools/complement/test/input_data/A.bed
@@ -0,0 +1 @@
+../../../../../tests/data/bed/A.bed
\ No newline at end of file
diff --git a/software/bedtools/complement/test/input_data/genome.sizes b/software/bedtools/complement/test/input_data/genome.sizes
deleted file mode 100644
index 8cc54558..00000000
--- a/software/bedtools/complement/test/input_data/genome.sizes
+++ /dev/null
@@ -1 +0,0 @@
-chr1	1780869
diff --git a/software/bedtools/complement/test/input_data/genome.sizes b/software/bedtools/complement/test/input_data/genome.sizes
new file mode 120000
index 00000000..3457e6c9
--- /dev/null
+++ b/software/bedtools/complement/test/input_data/genome.sizes
@@ -0,0 +1 @@
+../../../../../tests/data/bed/genome.sizes
\ No newline at end of file
diff --git a/software/bedtools/complement/test/main.nf b/software/bedtools/complement/test/main.nf
index e5722133..dfa024cc 100644
--- a/software/bedtools/complement/test/main.nf
+++ b/software/bedtools/complement/test/main.nf
@@ -2,9 +2,11 @@
 
 nextflow.preview.dsl = 2
 
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
 params.bedtools_complement_args = ''
 
-include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
 include BEDTOOLS_COMPLEMENT from '../main.nf' params(params)
 
 // Define input channels
@@ -14,5 +16,4 @@ chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
 // Run the workflow
 workflow {
     BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args)
-    // .check_output()
 }
diff --git a/software/bedtools/complement/test/nextflow.config b/software/bedtools/complement/test/nextflow.config
deleted file mode 100644
index c137a138..00000000
--- a/software/bedtools/complement/test/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'