feat: create bed2saf module

adapted from CCBR-1346 DDIS project

modules/CCBR/custom/bed2saf/main.nf

@@ -0,0 +1,35 @@
+process CUSTOM_BED2SAF {
+    label 'process_single'
+
+    input:
+    tuple val(meta), path(bed)
+
+    output:
+    tuple val(meta), path("*.saf"), emit: saf
+    path('versions.yml'), emit: versions
+
+    script:
+    def saf = "${bed.baseName}.saf"
+    """
+    #!/usr/bin/env python
+    import platform
+
+    with open("${saf}", 'w') as outfile:
+        outfile.write('\\t'.join(['GeneID', 'Chr', 'Start', 'End', 'Strand']))
+        with open("${bed}", 'r') as infile:
+            for line in infile:
+                (chr, start, end,) = line.strip().split('\\t')
+                peak_id = f'{chr}:{start}-{end}'
+                strand = '.' # no strand info available
+                outfile.write('\\t'.join([peak_id, chr, start, end, strand]) + '\\n')
+
+    with open("versions.yml", "w") as outfile:
+        outfile.write('"${task.process}":\\n')
+        outfile.write(f'  Python: "{platform.python_version()}"\\n')
+    """
+
+    stub:
+    """
+    touch ${bed.baseName}.saf versions.yml
+    """
+}

modules/CCBR/custom/bed2saf/meta.yml

@@ -0,0 +1,41 @@
+name: custom_bed2saf
+description: |
+  The module converts a BED file to SAF (simplified annotation format)
+
+keywords:
+  - bed
+  - saf
+tools:
+  - Python:
+      description: |
+        The Python Programming Language
+      homepage: https://www.python.org/
+      licence: ["Python License 2.0"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BED file
+      pattern: "*.bed"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - saf:
+      type: file
+      description: SAF file
+      pattern: "*.saf"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@kelly-sovacool"
+maintainers:
+  - "@kelly-sovacool"