Add singularity containers for rnaseq pipeline modules

software/fastqc/main.nf

@@ -12,7 +12,11 @@ process FASTQC {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
         container "quay.io/biocontainers/fastqc:0.11.9--0"
+    }
     
     input:
     tuple val(meta), path(reads)

software/gffread/main.nf

@@ -11,7 +11,11 @@ process GFFREAD {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
+    } else {
         container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
+    }
 
     input:
     path gff

software/hisat2/align/main.nf

@@ -14,7 +14,11 @@ process HISAT2_ALIGN {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    }
     
     input:
     tuple val(meta), path(reads)

software/hisat2/build/main.nf

@@ -13,7 +13,11 @@ process HISAT2_BUILD {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+    }
 
     input:
     path fasta

software/hisat2/extractsplicesites/main.nf

@@ -12,7 +12,11 @@ process HISAT2_EXTRACTSPLICESITES {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+    }
     
     input:
     path gtf

software/picard/markduplicates/main.nf

@@ -11,8 +11,12 @@ process PICARD_MARKDUPLICATES {
         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::picard=2.23.8" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
-    container "quay.io/biocontainers/picard:2.23.8--0"    
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
+    } else {
+        container "quay.io/biocontainers/picard:2.23.9--0"
+    }
 
     input:
     tuple val(meta), path(bam)

software/preseq/lcextrap/main.nf

@@ -13,7 +13,11 @@ process PRESEQ_LCEXTRAP {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
+    } else {
         container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
+    }
     
     input:
     tuple val(meta), path(bam)

software/qualimap/rnaseq/main.nf

@@ -12,7 +12,11 @@ process QUALIMAP_RNASEQ {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    } else {
         container "quay.io/biocontainers/qualimap:2.2.2d--1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rsem/calculateexpression/main.nf

@@ -12,7 +12,11 @@ process RSEM_CALCULATEEXPRESSION {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
 
     input:
     tuple val(meta), path(reads)

software/rsem/preparereference/main.nf

@@ -12,7 +12,11 @@ process RSEM_PREPAREREFERENCE {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
 
     input:
     path fasta

software/rseqc/bamstat/main.nf

@@ -12,7 +12,11 @@ process RSEQC_BAMSTAT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/inferexperiment/main.nf

@@ -12,7 +12,11 @@ process RSEQC_INFEREXPERIMENT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/innerdistance/main.nf

@@ -12,7 +12,11 @@ process RSEQC_INNERDISTANCE {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/junctionannotation/main.nf

@@ -12,7 +12,11 @@ process RSEQC_JUNCTIONANNOTATION {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/junctionsaturation/main.nf

@@ -12,7 +12,11 @@ process RSEQC_JUNCTIONSATURATION {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/readdistribution/main.nf

@@ -12,7 +12,11 @@ process RSEQC_READDISTRIBUTION {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/rseqc/readduplication/main.nf

@@ -12,7 +12,11 @@ process RSEQC_READDUPLICATION {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam)

software/salmon/index/main.nf

@@ -11,8 +11,12 @@ process SALMON_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
+    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
-    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
+    } else {
+        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
+    }
 
     input:
     path genome_fasta
@@ -38,7 +42,7 @@ process SALMON_INDEX {
     salmon \\
         index \\
         --threads $task.cpus \\
-        -t gentrome.fa \\
+        -t $gentrome \\
         -d decoys.txt \\
         $options.args \\
         -i salmon

software/salmon/quant/main.nf

@@ -11,8 +11,12 @@ process SALMON_QUANT {
         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::salmon=1.3.0" : null)
+    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
-    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
+    } else {
+        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
+    }
 
     input:
     tuple val(meta), path(reads)

software/samtools/flagstat/main.nf

@@ -10,7 +10,11 @@ process SAMTOOLS_FLAGSTAT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
 
     input:
     tuple val(meta), path(bam), path(bai)

software/samtools/idxstats/main.nf

@@ -10,7 +10,11 @@ process SAMTOOLS_IDXSTATS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
 
     input:
     tuple val(meta), path(bam), path(bai)

software/samtools/index/main.nf

@@ -10,7 +10,11 @@ process SAMTOOLS_INDEX {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
 
     input:
     tuple val(meta), path(bam)

software/samtools/sort/main.nf

@@ -12,7 +12,11 @@ process SAMTOOLS_SORT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
 
     input:
     tuple val(meta), path(bam)

software/samtools/stats/main.nf

@@ -10,7 +10,11 @@ process SAMTOOLS_STATS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
     
     input:
     tuple val(meta), path(bam), path(bai)

software/sortmerna/main.nf

@@ -12,7 +12,11 @@ process SORTMERNA {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+    } else {
         container "quay.io/biocontainers/sortmerna:4.2.0--0"
+    }
     
     input:
     tuple val(meta), path(reads)

software/star/align/main.nf

@@ -13,7 +13,12 @@ process STAR_ALIGN {
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         container "quay.io/biocontainers/star:2.6.1d--0"
+    }
+
 
     input:
     tuple val(meta), path(reads)

software/star/genomegenerate/main.nf

@@ -13,7 +13,11 @@ process STAR_GENOMEGENERATE {
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         container "quay.io/biocontainers/star:2.6.1d--0"
+    }
 
     input:
     path fasta

software/stringtie/main.nf

@@ -11,9 +11,12 @@ process STRINGTIE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    // Note: 2.7X indices incompatible with AWS iGenomes.
     conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+    } else {
         container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+    }
 
     input:
     tuple val(meta), path(bam)

software/subread/featurecounts/main.nf

@@ -11,9 +11,12 @@ process SUBREAD_FEATURECOUNTS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    // Note: 2.7X indices incompatible with AWS iGenomes.
     conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
+    } else {
         container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
+    }
 
     input:
     tuple val(meta), path(bams), path(annotation)

software/trimgalore/main.nf

@@ -12,7 +12,11 @@ process TRIMGALORE {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+    } else {
         container "quay.io/biocontainers/trim-galore:0.6.6--0"
+    }
 
     input:
     tuple val(meta), path(reads)

software/ucsc/bedgraphtobigwig/main.nf

@@ -14,7 +14,11 @@ process UCSC_BEDGRAPHTOBIGWIG {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    } else {
         container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    }
     
     input:
     tuple val(meta), path(bedgraph)

software/umitools/dedup/main.nf

@@ -11,8 +11,12 @@ process UMITOOLS_DEDUP {
         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::umi_tools=1.0.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
-    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+    } else {
+        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+    }
 
     input:
     tuple val(meta), path(bam), path(bai)

software/umitools/extract/main.nf

@@ -11,8 +11,12 @@ process UMITOOLS_EXTRACT {
         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::umi_tools=1.0.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
-    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+    } else {
+        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+    }
 
     input:
     tuple val(meta), path(reads)