Fixed intersect, complement indentation issues

software/bedtools/complement/main.nf

@@ -29,7 +29,13 @@ process BEDTOOLS_COMPLEMENT {
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-        bedtools complement -i $beds -g $sizes ${options.args} > ${prefix}.complement.bed
+    bedtools \\
+        complement \\
+        -i $beds \\
+        -g $sizes \\
+        $options.args \\
+        > ${prefix}.complement.bed
+
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """
 }

software/bedtools/complement/meta.yml

@@ -8,7 +8,6 @@ tools:
         description: |
             A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
         documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
-
 params:
     - outdir:
         type: string

software/bedtools/intersect/main.nf

@@ -25,7 +25,7 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path("*.intersect.bed"), emit: bed
     path  "*.version.txt", emit: version
 
-    script: // TODO change script to account for multiple possible intersections
+    script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """

software/bedtools/intersect/meta.yml

@@ -9,7 +9,6 @@ tools:
         description: |
             A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
         documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
-
 params:
     - outdir:
         type: string
@@ -33,10 +32,15 @@ input:
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+    - bed1:
         type: file
-        description: List of bed files
+        description: Bed file, each feature in 1 is compared to 2 in search of overlaps
         pattern: "*.{bed}"
+    - bed2:
+        type: file
+        description: Second bed file, used to compare to 1.
+        pattern: "*.{bed}"
+
 output:
     - meta:
         type: map
@@ -52,7 +56,6 @@ output:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
 authors:
     -"@Emiller88"
     -"@sruthipsuresh"