Updated test directory with input files, corrected main.nf and config. Additionally, main.nf for the process was updated.

software/bedtools/sloprefseq/test/input/A.bed

@@ -0,0 +1,5 @@
+chr1	951	1061
+chr1	1300	1420
+chr1	1400	1500
+
+

software/bedtools/sloprefseq/test/input/genome.sizes

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

software/bedtools/sloprefseq/test/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+include BEDTOOLS_SLOPREFSEQ from '../sloprefseq/main.nf' addParams( options: [publish_dir:'test_bed_file'])
+
+// Define input channels
+
+// Run the workflow
+workflow test_bed_file{
+    def input = []
+    input = [ [ id:'test' ], 
+              [ file("${baseDir}/input/A.bed", checkIfExists: true),
+                file("${baseDir}/input/genome.sizes", checkIfExists: true)] ]
+
+    BEDTOOLS_SLOPREFSEQ ( input )
+
+}
+
+workflow {
+    test_bed_file()
+}

software/bedtools/sloprefseq/test/nextflow.config

@@ -0,0 +1,19 @@
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    enable_conda = false
+}
+
+profiles {
+    conda  {
+        params.enable_conda = true
+    }
+    docker {
+        docker.enabled = true
+        docker.runOptions = '-u \$(id -u):\$(id -g)'
+    }
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+    }
+}