From 30e64becaa1e6c807a09a49a6d3d457ff3cf7251 Mon Sep 17 00:00:00 2001
From: Mei Wu <25568561+projectoriented@users.noreply.github.com>
Date: Tue, 11 Jan 2022 22:31:37 +0100
Subject: [PATCH] ucsc/wigtobigwig: add meta map (#1199)

* add meta info

* updated meta.yml

* Apply suggestions from code review

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/ucsc/wigtobigwig/main.nf        | 11 ++++++-----
 modules/ucsc/wigtobigwig/meta.yml       |  6 ++++++
 tests/modules/ucsc/wigtobigwig/main.nf  |  3 ++-
 tests/modules/ucsc/wigtobigwig/test.yml |  2 ++
 4 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf
index 4c596c9a..6a1847b6 100644
--- a/modules/ucsc/wigtobigwig/main.nf
+++ b/modules/ucsc/wigtobigwig/main.nf
@@ -1,7 +1,7 @@
 def VERSION = '377' // Version information not provided by tool on CLI
 
 process UCSC_WIGTOBIGWIG {
-    tag '$wig'
+    tag "$meta.id"
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
@@ -10,21 +10,22 @@ process UCSC_WIGTOBIGWIG {
         'quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2' }"
 
     input:
-    path wig
+    tuple val(meta), path(wig)
     path sizes
 
     output:
-    path "*.bw"        , emit: bw
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.bw"), emit: bw
+    path "versions.yml"          , emit: versions
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     wigToBigWig \\
         $args \\
         $wig \\
         $sizes \\
-        ${wig.getSimpleName()}.bw
+        ${prefix}.bw
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/ucsc/wigtobigwig/meta.yml b/modules/ucsc/wigtobigwig/meta.yml
index 4723ff2b..5ca94bb4 100644
--- a/modules/ucsc/wigtobigwig/meta.yml
+++ b/modules/ucsc/wigtobigwig/meta.yml
@@ -15,6 +15,11 @@ tools:
       licence: ['varies; see http://genome.ucsc.edu/license']
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - wig:
       type: file
       description: wig file
@@ -35,3 +40,4 @@ output:
 
 authors:
   - "@jianhong"
+  - "@projectoriented"
diff --git a/tests/modules/ucsc/wigtobigwig/main.nf b/tests/modules/ucsc/wigtobigwig/main.nf
index 614d4150..2abbe5b2 100644
--- a/tests/modules/ucsc/wigtobigwig/main.nf
+++ b/tests/modules/ucsc/wigtobigwig/main.nf
@@ -6,7 +6,8 @@ include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf'
 
 workflow test_ucsc_wigtobigwig {
 
-    input = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
+    input = [ [ id:'test', single_end:false ], // meta map,
+                file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true) ]
 
     sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
 
diff --git a/tests/modules/ucsc/wigtobigwig/test.yml b/tests/modules/ucsc/wigtobigwig/test.yml
index 08d4bce4..ea1e12b0 100644
--- a/tests/modules/ucsc/wigtobigwig/test.yml
+++ b/tests/modules/ucsc/wigtobigwig/test.yml
@@ -6,3 +6,5 @@
   files:
     - path: output/ucsc/test.bw
       md5sum: b64af7003665dc51fae958216b06ed95
+    - path: output/ucsc/versions.yml
+      md5sum: 7e14421c65faf5165389f34806acdb12