diff --git a/software/fastqc/main.nf b/software/fastqc/main.nf
index 3edc97a1..3cb510ac 100644
--- a/software/fastqc/main.nf
+++ b/software/fastqc/main.nf
@@ -11,8 +11,12 @@ process FASTQC {
         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::fastqc=0.11.9" : null)
-    container "quay.io/biocontainers/fastqc:0.11.9--0"
+    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)
diff --git a/software/gffread/main.nf b/software/gffread/main.nf
index 9906f620..0e446ac8 100644
--- a/software/gffread/main.nf
+++ b/software/gffread/main.nf
@@ -10,8 +10,12 @@ process GFFREAD {
         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::gffread=0.12.1" : null)
-    container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
+    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
diff --git a/software/hisat2/align/main.nf b/software/hisat2/align/main.nf
index d2c6fbcd..ef37b7b7 100644
--- a/software/hisat2/align/main.nf
+++ b/software/hisat2/align/main.nf
@@ -13,9 +13,13 @@ process HISAT2_ALIGN {
         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::hisat2=2.2.0 bioconda::samtools=1.10" : null)
-    container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
-
+    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)
     path  index
diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf
index 25596c89..5d83118c 100644
--- a/software/hisat2/build/main.nf
+++ b/software/hisat2/build/main.nf
@@ -12,8 +12,12 @@ process HISAT2_BUILD {
         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::hisat2=2.2.0" : null)
-    container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+    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
diff --git a/software/hisat2/extractsplicesites/main.nf b/software/hisat2/extractsplicesites/main.nf
index bfd2cf38..665f4703 100644
--- a/software/hisat2/extractsplicesites/main.nf
+++ b/software/hisat2/extractsplicesites/main.nf
@@ -11,9 +11,13 @@ process HISAT2_EXTRACTSPLICESITES {
         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::hisat2=2.2.0" : null)
-    container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
-
+    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
 
diff --git a/software/picard/markduplicates/main.nf b/software/picard/markduplicates/main.nf
index 032a4070..33245e0a 100644
--- a/software/picard/markduplicates/main.nf
+++ b/software/picard/markduplicates/main.nf
@@ -10,9 +10,13 @@ process PICARD_MARKDUPLICATES {
     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::picard=2.23.8" : null)
-    container "quay.io/biocontainers/picard:2.23.8--0"    
+    
+    conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
+    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)
diff --git a/software/preseq/lcextrap/main.nf b/software/preseq/lcextrap/main.nf
index 89afeda7..56645274 100644
--- a/software/preseq/lcextrap/main.nf
+++ b/software/preseq/lcextrap/main.nf
@@ -12,9 +12,13 @@ process PRESEQ_LCEXTRAP {
         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::preseq=2.0.3" : null)
-    container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
-
+    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)
     
diff --git a/software/qualimap/rnaseq/main.nf b/software/qualimap/rnaseq/main.nf
index f24001e8..adbc7865 100644
--- a/software/qualimap/rnaseq/main.nf
+++ b/software/qualimap/rnaseq/main.nf
@@ -11,8 +11,12 @@ process QUALIMAP_RNASEQ {
         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::qualimap=2.2.2d" : null)
-    container "quay.io/biocontainers/qualimap:2.2.2d--1"
+    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)
diff --git a/software/rsem/calculateexpression/main.nf b/software/rsem/calculateexpression/main.nf
index f00d7686..478670d0 100644
--- a/software/rsem/calculateexpression/main.nf
+++ b/software/rsem/calculateexpression/main.nf
@@ -11,8 +11,12 @@ process RSEM_CALCULATEEXPRESSION {
         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::rsem=1.3.3 bioconda::star=2.7.6a" : null)
-    container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    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)
diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf
index 982f6cdd..3aceed8c 100644
--- a/software/rsem/preparereference/main.nf
+++ b/software/rsem/preparereference/main.nf
@@ -11,8 +11,12 @@ process RSEM_PREPAREREFERENCE {
         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::rsem=1.3.3 bioconda::star=2.7.6a" : null)
-    container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    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
diff --git a/software/rseqc/bamstat/main.nf b/software/rseqc/bamstat/main.nf
index e9a34add..f6525cd0 100644
--- a/software/rseqc/bamstat/main.nf
+++ b/software/rseqc/bamstat/main.nf
@@ -11,8 +11,12 @@ process RSEQC_BAMSTAT {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/inferexperiment/main.nf b/software/rseqc/inferexperiment/main.nf
index 79dfd4f9..4f35d3e3 100644
--- a/software/rseqc/inferexperiment/main.nf
+++ b/software/rseqc/inferexperiment/main.nf
@@ -11,8 +11,12 @@ process RSEQC_INFEREXPERIMENT {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/innerdistance/main.nf b/software/rseqc/innerdistance/main.nf
index 9ace426d..8273b353 100644
--- a/software/rseqc/innerdistance/main.nf
+++ b/software/rseqc/innerdistance/main.nf
@@ -11,8 +11,12 @@ process RSEQC_INNERDISTANCE {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/junctionannotation/main.nf b/software/rseqc/junctionannotation/main.nf
index 9cc6d00f..a12782f0 100644
--- a/software/rseqc/junctionannotation/main.nf
+++ b/software/rseqc/junctionannotation/main.nf
@@ -11,8 +11,12 @@ process RSEQC_JUNCTIONANNOTATION {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/junctionsaturation/main.nf b/software/rseqc/junctionsaturation/main.nf
index a472aba5..e607c822 100644
--- a/software/rseqc/junctionsaturation/main.nf
+++ b/software/rseqc/junctionsaturation/main.nf
@@ -11,8 +11,12 @@ process RSEQC_JUNCTIONSATURATION {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/readdistribution/main.nf b/software/rseqc/readdistribution/main.nf
index de99185f..b248fc65 100644
--- a/software/rseqc/readdistribution/main.nf
+++ b/software/rseqc/readdistribution/main.nf
@@ -11,8 +11,12 @@ process RSEQC_READDISTRIBUTION {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/rseqc/readduplication/main.nf b/software/rseqc/readduplication/main.nf
index 4a3998da..23bc602c 100644
--- a/software/rseqc/readduplication/main.nf
+++ b/software/rseqc/readduplication/main.nf
@@ -11,8 +11,12 @@ process RSEQC_READDUPLICATION {
         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::rseqc=3.0.1" : null)
-    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    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)
diff --git a/software/salmon/index/main.nf b/software/salmon/index/main.nf
index ef6ce209..5349d6ce 100644
--- a/software/salmon/index/main.nf
+++ b/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)
-    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
+    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
@@ -38,10 +42,10 @@ process SALMON_INDEX {
     salmon \\
         index \\
         --threads $task.cpus \\
-        -t gentrome.fa \\
+        -t $gentrome \\
         -d decoys.txt \\
         $options.args \\
         -i salmon
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
     """
-}
\ No newline at end of file
+}
diff --git a/software/salmon/quant/main.nf b/software/salmon/quant/main.nf
index bb0d07d9..42874e0b 100644
--- a/software/salmon/quant/main.nf
+++ b/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)
-    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
+    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)
diff --git a/software/samtools/flagstat/main.nf b/software/samtools/flagstat/main.nf
index 46e95df0..e23f0864 100644
--- a/software/samtools/flagstat/main.nf
+++ b/software/samtools/flagstat/main.nf
@@ -9,8 +9,12 @@ process SAMTOOLS_FLAGSTAT {
         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::samtools=1.10" : null)
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    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)
diff --git a/software/samtools/idxstats/main.nf b/software/samtools/idxstats/main.nf
index 29e680df..40ac4702 100644
--- a/software/samtools/idxstats/main.nf
+++ b/software/samtools/idxstats/main.nf
@@ -9,8 +9,12 @@ process SAMTOOLS_IDXSTATS {
         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::samtools=1.10" : null)
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    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)
diff --git a/software/samtools/index/main.nf b/software/samtools/index/main.nf
index 23c9ec41..c0dadfd5 100644
--- a/software/samtools/index/main.nf
+++ b/software/samtools/index/main.nf
@@ -9,8 +9,12 @@ process SAMTOOLS_INDEX {
         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::samtools=1.10" : null)
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    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)
diff --git a/software/samtools/sort/main.nf b/software/samtools/sort/main.nf
index a872e11f..e43e4a9b 100644
--- a/software/samtools/sort/main.nf
+++ b/software/samtools/sort/main.nf
@@ -11,8 +11,12 @@ process SAMTOOLS_SORT {
         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::samtools=1.10" : null)
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    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)
diff --git a/software/samtools/stats/main.nf b/software/samtools/stats/main.nf
index e1949ee7..ba38c6ad 100644
--- a/software/samtools/stats/main.nf
+++ b/software/samtools/stats/main.nf
@@ -9,9 +9,13 @@ process SAMTOOLS_STATS {
         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::samtools=1.10" : null)
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-
+    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)
     
diff --git a/software/sortmerna/main.nf b/software/sortmerna/main.nf
index a1ea4864..5f2c34f9 100644
--- a/software/sortmerna/main.nf
+++ b/software/sortmerna/main.nf
@@ -11,9 +11,13 @@ process SORTMERNA {
         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::sortmerna=4.2.0" : null)
-    container "quay.io/biocontainers/sortmerna:4.2.0--0"
-
+    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)
     path  fasta
diff --git a/software/star/align/main.nf b/software/star/align/main.nf
index c143ba1d..866608d8 100644
--- a/software/star/align/main.nf
+++ b/software/star/align/main.nf
@@ -12,8 +12,13 @@ process STAR_ALIGN {
         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::star=2.6.1d" : null)
-    container "quay.io/biocontainers/star:2.6.1d--0"
+    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)
diff --git a/software/star/genomegenerate/main.nf b/software/star/genomegenerate/main.nf
index 915b5675..e9aa1234 100644
--- a/software/star/genomegenerate/main.nf
+++ b/software/star/genomegenerate/main.nf
@@ -12,8 +12,12 @@ process STAR_GENOMEGENERATE {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda     (params.enable_conda ? "bioconda::star=2.6.1d" : null)
-    container "quay.io/biocontainers/star:2.6.1d--0"
+    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
diff --git a/software/stringtie/main.nf b/software/stringtie/main.nf
index ba2c42bd..35f5eab8 100644
--- a/software/stringtie/main.nf
+++ b/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)
-    container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+    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)
diff --git a/software/subread/featurecounts/main.nf b/software/subread/featurecounts/main.nf
index e8644af5..55ad94b1 100644
--- a/software/subread/featurecounts/main.nf
+++ b/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)
-    container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
+    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)
diff --git a/software/trimgalore/main.nf b/software/trimgalore/main.nf
index 742ffaf5..79cc7456 100644
--- a/software/trimgalore/main.nf
+++ b/software/trimgalore/main.nf
@@ -11,8 +11,12 @@ process TRIMGALORE {
         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::trim-galore=0.6.6" : null)
-    container "quay.io/biocontainers/trim-galore:0.6.6--0"
+    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)
diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf
index 873481cf..4a8e95e9 100644
--- a/software/ucsc/bedgraphtobigwig/main.nf
+++ b/software/ucsc/bedgraphtobigwig/main.nf
@@ -13,9 +13,13 @@ process UCSC_BEDGRAPHTOBIGWIG {
         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::ucsc-bedgraphtobigwig=377" : null)
-    container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
-
+    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)
     path  sizes
diff --git a/software/umitools/dedup/main.nf b/software/umitools/dedup/main.nf
index 8348cda4..ce1dd987 100644
--- a/software/umitools/dedup/main.nf
+++ b/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)
-    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    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)
diff --git a/software/umitools/extract/main.nf b/software/umitools/extract/main.nf
index d04f2e3d..eb1372a5 100644
--- a/software/umitools/extract/main.nf
+++ b/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)
-    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    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)