From 2959b4ba070d138d1577acc48d35cc669fbef972 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Fri, 29 Oct 2021 13:22:17 +0100
Subject: [PATCH] Bedtools sort add extension choice input (#984)

* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Added extension input for bedtools sort

* whitespace

* Updated docs

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
---
 modules/bedtools/sort/main.nf        | 11 ++++++-----
 modules/bedtools/sort/meta.yml       | 19 +++++++++++++------
 tests/modules/bedtools/sort/main.nf  |  2 +-
 tests/modules/bedtools/sort/test.yml |  2 +-
 4 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf
index bdba3376..4a51c4b2 100644
--- a/modules/bedtools/sort/main.nf
+++ b/modules/bedtools/sort/main.nf
@@ -19,20 +19,21 @@ process BEDTOOLS_SORT {
     }
 
     input:
-    tuple val(meta), path(bed)
+    tuple val(meta), path(intervals)
+    val   extension
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.${extension}"), emit: sorted
+    path  "versions.yml"                   , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bedtools \\
         sort \\
-        -i $bed \\
+        -i $intervals \\
         $options.args \\
-        > ${prefix}.bed
+        > ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/modules/bedtools/sort/meta.yml b/modules/bedtools/sort/meta.yml
index 5b8b41d7..c7b1b098 100644
--- a/modules/bedtools/sort/meta.yml
+++ b/modules/bedtools/sort/meta.yml
@@ -15,20 +15,26 @@ input:
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+    - intervals:
         type: file
-        description: Input BED file
-        pattern: "*.{bed}"
+        description: BED/BEDGRAPH
+        pattern: "*.{bed|bedGraph}"
+
+    - extension:
+        type: string
+        description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
 output:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+
+    - sorted:
         type: file
-        description: Sorted BED file
-        pattern: "*.{bed}"
+        description: Sorted output file
+        pattern: "*.${extension}"
+
     - versions:
         type: file
         description: File containing software versions
@@ -37,3 +43,4 @@ authors:
     - "@Emiller88"
     - "@sruthipsuresh"
     - "@drpatelh"
+    - "@chris-cheshire"
diff --git a/tests/modules/bedtools/sort/main.nf b/tests/modules/bedtools/sort/main.nf
index ad1a3df4..b5d34e2f 100644
--- a/tests/modules/bedtools/sort/main.nf
+++ b/tests/modules/bedtools/sort/main.nf
@@ -9,5 +9,5 @@ workflow test_bedtools_sort {
               file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
             ]
 
-    BEDTOOLS_SORT ( input )
+    BEDTOOLS_SORT ( input, "testext" )
 }
diff --git a/tests/modules/bedtools/sort/test.yml b/tests/modules/bedtools/sort/test.yml
index ceb25f7d..1dd04507 100644
--- a/tests/modules/bedtools/sort/test.yml
+++ b/tests/modules/bedtools/sort/test.yml
@@ -4,5 +4,5 @@
     - bedtools
     - bedtools/sort
   files:
-    - path: ./output/bedtools/test_out.bed
+    - path: ./output/bedtools/test_out.testext
       md5sum: fe4053cf4de3aebbdfc3be2efb125a74