Update main.nf

modules/bustools/sort/main.nf

@@ -1,23 +1,6 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/software
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided as a string i.e. "options.args"
-//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 params.options = [:]
 options        = initOptions(params.options)
 
@@ -39,14 +22,14 @@ process BUSTOOLS_SORT {
     tuple val(meta), path(bus)
 
     output:
-    tuple val(meta), path("${prefix}.sorted.bus"), emit: bus
+    tuple val(meta), path("*.bus"), emit: bus
     path  "versions.yml"          , emit: versions
 
     script:
     prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bustools sort \\
-        -o ${prefix}.sorted.bus \\
+        -o ${prefix}.bus \\
         -t $task.cpus \\
         -m ${task.memory.toGiga()}G \\
         $options.args \\