From 70de0331a5a73984ad6705d1cb0b32bc70a63676 Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Fri, 8 Jan 2021 13:44:02 -0600
Subject: [PATCH] Corrected pytest and config

---
 .github/workflows/bedtools_merge.yml      | 2 +-
 .github/workflows/bedtools_slop.yml       | 2 +-
 .github/workflows/bedtools_sort.yml       | 2 +-
 software/bedtools/complement/functions.nf | 2 +-
 software/bedtools/complement/main.nf      | 2 +-
 software/bedtools/genomecov/functions.nf  | 2 +-
 software/bedtools/intersect/functions.nf  | 2 +-
 software/bedtools/intersect/main.nf       | 2 +-
 software/bedtools/merge/functions.nf      | 2 +-
 software/bedtools/slop/functions.nf       | 2 +-
 software/bedtools/slop/main.nf            | 4 ++--
 software/bedtools/sort/functions.nf       | 2 +-
 12 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/bedtools_merge.yml b/.github/workflows/bedtools_merge.yml
index 6286931a..38ec37df 100644
--- a/.github/workflows/bedtools_merge.yml
+++ b/.github/workflows/bedtools_merge.yml
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_merge--symlink --wt 2
+      - run: pytest --tag bedtools_merge --symlink --wt 2
diff --git a/.github/workflows/bedtools_slop.yml b/.github/workflows/bedtools_slop.yml
index b3b03813..7cd6f056 100644
--- a/.github/workflows/bedtools_slop.yml
+++ b/.github/workflows/bedtools_slop.yml
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_slop--symlink --wt 2
+      - run: pytest --tag bedtools_slop --symlink --wt 2
diff --git a/.github/workflows/bedtools_sort.yml b/.github/workflows/bedtools_sort.yml
index e3a194b2..ee14f308 100644
--- a/.github/workflows/bedtools_sort.yml
+++ b/.github/workflows/bedtools_sort.yml
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_sort--symlink --wt 2
+      - run: pytest --tag bedtools_sort --symlink --wt 2
diff --git a/software/bedtools/complement/functions.nf b/software/bedtools/complement/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/complement/functions.nf
+++ b/software/bedtools/complement/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bedtools/complement/main.nf b/software/bedtools/complement/main.nf
index c77df40f..2884f3b8 100644
--- a/software/bedtools/complement/main.nf
+++ b/software/bedtools/complement/main.nf
@@ -16,7 +16,7 @@ process BEDTOOLS_COMPLEMENT {
     } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
-    
+
     input:
         tuple val(meta), path(beds), path (sizes)
 
diff --git a/software/bedtools/genomecov/functions.nf b/software/bedtools/genomecov/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/genomecov/functions.nf
+++ b/software/bedtools/genomecov/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bedtools/intersect/functions.nf b/software/bedtools/intersect/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/intersect/functions.nf
+++ b/software/bedtools/intersect/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bedtools/intersect/main.nf b/software/bedtools/intersect/main.nf
index 1edeb505..50e00b3b 100644
--- a/software/bedtools/intersect/main.nf
+++ b/software/bedtools/intersect/main.nf
@@ -9,7 +9,7 @@ process BEDTOOLS_INTERSECT {
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-    
+
     conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
diff --git a/software/bedtools/merge/functions.nf b/software/bedtools/merge/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/merge/functions.nf
+++ b/software/bedtools/merge/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bedtools/slop/functions.nf b/software/bedtools/slop/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/slop/functions.nf
+++ b/software/bedtools/slop/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/software/bedtools/slop/main.nf b/software/bedtools/slop/main.nf
index 88027244..dcf3c5bc 100644
--- a/software/bedtools/slop/main.nf
+++ b/software/bedtools/slop/main.nf
@@ -16,7 +16,7 @@ process BEDTOOLS_SLOP {
     } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
-    
+
 
     input:
         tuple val(meta), path(beds), path (sizes)
@@ -42,6 +42,6 @@ process BEDTOOLS_SLOP {
         """
         slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
-        """       
+        """
         }
 }
diff --git a/software/bedtools/sort/functions.nf b/software/bedtools/sort/functions.nf
index 54dc8fe8..d25eea86 100644
--- a/software/bedtools/sort/functions.nf
+++ b/software/bedtools/sort/functions.nf
@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
\ No newline at end of file
+}