From e360617ac6a9ce7308713081dd5d3263f3c7168d Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Thu, 28 Jan 2021 08:24:33 -0600
Subject: [PATCH] Fixed images, genomecov

---
 software/bedtools/genomecov/main.nf  | 27 ++++++++++++++++-----------
 software/bedtools/genomecov/meta.yml |  4 ++--
 software/bedtools/slop/main.nf       |  2 +-
 software/bedtools/slop/meta.yml      |  2 +-
 tests/software/bedtools/main.nf      |  4 +---
 5 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/software/bedtools/genomecov/main.nf b/software/bedtools/genomecov/main.nf
index 233469a7..3e0c0e9d 100644
--- a/software/bedtools/genomecov/main.nf
+++ b/software/bedtools/genomecov/main.nf
@@ -13,23 +13,28 @@ process BEDTOOLS_GENOMECOV {
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
-        container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
 
     input:
-        tuple val(meta), path(bams), path (sizes)
+    tuple val(meta), path(bams)
 
     output:
-        tuple val(meta), path("*.bed"), emit: coverage
-        path  "*.version.txt", emit: version
+    tuple val(meta), path("*.bed"), emit: coverage
+    path  "*.version.txt", emit: version
 
     script:
-        def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        """
-        bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.bed
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
-        """
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedtools \\
+        genomecov \\
+        -ibam $bams \\
+        $options.args \\
+        > ${prefix}.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
 }
diff --git a/software/bedtools/genomecov/meta.yml b/software/bedtools/genomecov/meta.yml
index 02430948..138c9e29 100644
--- a/software/bedtools/genomecov/meta.yml
+++ b/software/bedtools/genomecov/meta.yml
@@ -36,7 +36,7 @@ input:
     - bam:
         type: file
         description: List of bam files
-        pattern: "*.{bed}"
+        pattern: "*.{bam}"
 output:
     - meta:
         type: map
@@ -45,7 +45,7 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Computed bed file
+        description: Computed genomecov bed file
         pattern: "*.{bed}"
 
     - version:
diff --git a/software/bedtools/slop/main.nf b/software/bedtools/slop/main.nf
index 51bd7dcc..cd13fae3 100644
--- a/software/bedtools/slop/main.nf
+++ b/software/bedtools/slop/main.nf
@@ -13,7 +13,7 @@ process BEDTOOLS_SLOP {
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
         container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
diff --git a/software/bedtools/slop/meta.yml b/software/bedtools/slop/meta.yml
index 4f8b9840..1484d02c 100644
--- a/software/bedtools/slop/meta.yml
+++ b/software/bedtools/slop/meta.yml
@@ -64,7 +64,7 @@ output:
   - bed:
       type: file
       description: Edited bed file
-      pattern: "*.{slopbed}"
+      pattern: "*.{slop.bed}"
 
   - version:
       type: file
diff --git a/tests/software/bedtools/main.nf b/tests/software/bedtools/main.nf
index 51a39aa1..a523f5b4 100644
--- a/tests/software/bedtools/main.nf
+++ b/tests/software/bedtools/main.nf
@@ -22,8 +22,7 @@ workflow test_bedtools_complement {
 workflow test_bedtools_genomecov {
     def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
-              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
 
     BEDTOOLS_GENOMECOV( input )
 }
@@ -38,7 +37,6 @@ workflow test_bedtools_intersect {
 }
 
 
-//  TODO use output of sort module
 workflow test_bedtools_merge {
     def input = []
     input = [ [ id:'test' ], // meta map