From 2ade120249b92e382f964bd75701befa2c2dc75d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Fri, 16 Jul 2021 14:21:08 +0100
Subject: [PATCH] Add --paired flag to umitools dedup and bump to 1.1.2 (#583)

* Add --paired flag to umitools dedup and bump to 1.1.2

* paired not paired_end

* Fix ECLint
---
 modules/umitools/dedup/main.nf   | 14 +++++++-------
 modules/umitools/extract/main.nf | 10 +++++-----
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf
index 93ea6d45..f30ab164 100644
--- a/modules/umitools/dedup/main.nf
+++ b/modules/umitools/dedup/main.nf
@@ -11,11 +11,11 @@ process UMITOOLS_DEDUP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
     } else {
-        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+        container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
     }
 
     input:
@@ -23,19 +23,19 @@ process UMITOOLS_DEDUP {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.tsv"), emit: tsv
     path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def paired   = meta.single_end ? "" : "--paired"
     """
     umi_tools dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
-        --output-stats=$prefix \\
-        $options.args \\
+        $paired \\
+        $options.args
 
-    umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+    echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
     """
 }
diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf
index 581f41c3..e5c4e21c 100644
--- a/modules/umitools/extract/main.nf
+++ b/modules/umitools/extract/main.nf
@@ -11,11 +11,11 @@ process UMITOOLS_EXTRACT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
     } else {
-        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+        container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
     }
 
     input:
@@ -38,7 +38,7 @@ process UMITOOLS_EXTRACT {
             $options.args \\
             > ${prefix}.umi_extract.log
 
-        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
         """
     }  else {
         """
@@ -51,7 +51,7 @@ process UMITOOLS_EXTRACT {
             $options.args \\
             > ${prefix}.umi_extract.log
 
-        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
         """
     }
 }