Bedtools genomecov adapted to the current module standard

software/bedtools/genomecov/Dockerfile

@@ -4,4 +4,4 @@ LABEL authors="Jose Espinosa-Carrasco" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-bedtools-complementbed/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-bedtools-genomecov/bin:$PATH

software/bedtools/genomecov/main.nf

@@ -1,18 +1,33 @@
+def MODULE = "bedtools_genomecov"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
 process BEDTOOLS_GENOMECOV {
     tag {bam}
 
+    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 (bam)
     path (chrom_sizes)
     val (bedtools_genomecov_args)
 
     output:
-    stdout()
+    path "${bam}.bed", emit: coverage
+    path "*.version.txt", emit: version
 
     script:
     """
-    bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${bedtools_genomecov_args}
+    bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${bedtools_genomecov_args} > ${bam}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }

software/bedtools/genomecov/test/input_data/JK2067_downsampled_s0.1.bam

@@ -0,0 +1 @@
+../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

software/bedtools/genomecov/test/input_data/genome.sizes

@@ -1 +0,0 @@
-chr1	1780869

software/bedtools/genomecov/test/input_data/genome.sizes

@@ -0,0 +1 @@
+../../../../../tests/data/bed/genome.sizes

software/bedtools/genomecov/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_genomecov_args = '' //'-bg'
 
-include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
 include BEDTOOLS_GENOMECOV 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_GENOMECOV(ch_input, chrom_sizes, params.bedtools_genomecov_args)
-    // .check_output()
 }

software/bedtools/genomecov/test/nextflow.config

@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'