diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 999137563..e4ce0ae2d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '']
+        nxf_ver: ['20.11.0-edge']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -39,7 +39,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -71,7 +71,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -98,7 +98,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -123,7 +123,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -148,7 +148,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     steps:
       - name: Check out pipeline code
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b014db88d..6b0fc7d12 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,16 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.1dev - [date]
+## [[3.0](https://github.com/nf-core/rnaseq/releases/tag/3.0)] - 2020-12-15
 
-### Major enhancements
+### :warning: Major enhancements
 
-* The aligned BAM files generated by `--aligner star` will now be quantified using Salmon instead of featureCounts. As a result, the name of this option has now been changed to `--aligner star_salmon` and this will now be the default route through the pipeline. This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see [Zhao et al., 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001) and [Soneson et al., 2015](https://f1000research.com/articles/4-1521/v1)).
-* For similar reasons, quantification will not be performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.
+* You will need to install Nextflow `>=20.11.0-edge` to run the pipeline. If you are using Singularity, then features introduced in that release now enable the pipeline to directly download Singularity images hosted by Biocontainers as opposed to performing a conversion from Docker images (see [#496](https://github.com/nf-core/rnaseq/issues/496)).
+* The previous default of aligning BAM files using STAR and quantifying using featureCounts (`--aligner star`) has been removed. The new default is to align with STAR and quantify using Salmon (`--aligner star_salmon`).
+  * This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see [Zhao et al., 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001) and [Soneson et al., 2015](https://f1000research.com/articles/4-1521/v1)).
+* For similar reasons, **quantification will not be performed** if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments.
+  * This pipeline option is still available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2. No gene-level quantification results will be generated.
+  * In a future release we hope to add back quantitation for HISAT2 using different tools.
 
 ### Enhancements & fixes
 
 * Updated pipeline template to nf-core/tools `1.12.1`
+* Bump Nextflow version `20.07.1` -> `20.11.0-edge`
+* [[#494](https://github.com/nf-core/rnaseq/issues/494)] - Issue running rnaseq v2.0 (DSL2) with test profile
+* [[#496](https://github.com/nf-core/rnaseq/issues/496)] - Direct download of Singularity images via HTTPS
 * [[#498](https://github.com/nf-core/rnaseq/issues/498)] - Significantly different versions of STAR in star_rsem (2.7.6a) and star (2.6.1d)
 * [[#499](https://github.com/nf-core/rnaseq/issues/499)] - Use of salmon counts for DESeq2
 * [[#500](https://github.com/nf-core/rnaseq/issues/500), [#509](https://github.com/nf-core/rnaseq/issues/509)] - Error with AWS batch params
@@ -22,13 +29,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter                | New parameter               |
-|------------------------------|-----------------------------|
-| `--fc_extra_attributes`      | `--gtf_extra_attributes`    |
-| `--fc_group_features`        | `--gtf_group_features`      |
-| `--fc_count_type`            | `--gtf_count_type`          |
-| `--fc_group_features_type`   | `--gtf_group_features_type` |
-| `--skip_featurecounts`       | `-`                         |
+| Old parameter                | New parameter                         |
+|------------------------------|---------------------------------------|
+| `--fc_extra_attributes`      | `--gtf_extra_attributes`              |
+| `--fc_group_features`        | `--gtf_group_features`                |
+| `--fc_count_type`            | `--gtf_count_type`                    |
+| `--fc_group_features_type`   | `--gtf_group_features_type`           |
+|                              | `--singularity_pull_docker_container` |
+| `--skip_featurecounts`       |                                       |
 
 > **NB:** Parameter has been __updated__ if both old and new parameter information is present.  
 > **NB:** Parameter has been __added__ if just the new parameter information is present.  
diff --git a/README.md b/README.md
index d8d07812d..b5abdd3b5 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A520.07.1-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A520.11.0--edge-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -64,7 +64,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s
     ```
 
     > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-    > * If you are using `singularity`, it is highly recommended to use the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) settings to store the images in a central location for future pipeline runs.
+    > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. It is also highly recommended to use the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) settings to store the images in a central location for future pipeline runs.
     > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
diff --git a/conf/modules.config b/conf/modules.config
index de4a28324..6130febb7 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -63,12 +63,11 @@ params {
             publish_dir   = "genome/index"
         }
         'star_align' {
-            args          = "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0"
+            args          = "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend"
             publish_dir   = "${params.aligner}"
             publish_files = ['out':'log', 'tab':'log']
         }
         'star_salmon_quant' {
-            args          = "--seqBias --useVBOpt --gcBias"
             publish_dir   = "${params.aligner}"
         }
         'star_salmon_tximport' {
@@ -107,7 +106,7 @@ params {
             publish_dir   = "genome/index"
         }
         'salmon_quant' {
-            args          = "--validateMappings --seqBias --useVBOpt --gcBias"
+            args          = ""
         }
         'salmon_tximport' {
             publish_by_id = true
diff --git a/modules/local/process/bedtools_genomecov.nf b/modules/local/process/bedtools_genomecov.nf
index 2b74cd757..c43d47814 100644
--- a/modules/local/process/bedtools_genomecov.nf
+++ b/modules/local/process/bedtools_genomecov.nf
@@ -11,9 +11,13 @@ process BEDTOOLS_GENOMECOV {
         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)
-    container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
-
+    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"
+    } else {
+        container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
+    
     input:
     tuple val(meta), path(bam)
     
diff --git a/modules/local/process/cat_additional_fasta.nf b/modules/local/process/cat_additional_fasta.nf
index b4bd104c6..cafb91a70 100644
--- a/modules/local/process/cat_additional_fasta.nf
+++ b/modules/local/process/cat_additional_fasta.nf
@@ -12,8 +12,12 @@ process CAT_ADDITIONAL_FASTA {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     input:
     path fasta
diff --git a/modules/local/process/cat_fastq.nf b/modules/local/process/cat_fastq.nf
index 4270303fa..6351a21f4 100644
--- a/modules/local/process/cat_fastq.nf
+++ b/modules/local/process/cat_fastq.nf
@@ -13,8 +13,12 @@ process CAT_FASTQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/process/deseq2_qc.nf b/modules/local/process/deseq2_qc.nf
index 91e42e13e..14275a690 100644
--- a/modules/local/process/deseq2_qc.nf
+++ b/modules/local/process/deseq2_qc.nf
@@ -11,9 +11,13 @@ process DESEQ2_QC {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::r-base=4.0.3 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.2 conda-forge::r-rcolorbrewer=1.1_2 conda-forge::r-pheatmap=1.0.12 bioconda::bioconductor-deseq2=1.28.0 bioconda::bioconductor-biocparallel=1.22.0 bioconda::bioconductor-tximport=1.16.0 bioconda::bioconductor-complexheatmap=2.4.2" : null)
-    container "quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0"
-    
+    conda (params.enable_conda ? "conda-forge::r-base=4.0.3 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.2 conda-forge::r-rcolorbrewer=1.1_2 conda-forge::r-pheatmap=1.0.12 bioconda::bioconductor-deseq2=1.28.0 bioconda::bioconductor-biocparallel=1.22.0 bioconda::bioconductor-tximport=1.16.0 bioconda::bioconductor-complexheatmap=2.4.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0"
+    }
+
     input:
     path counts
     path pca_header_multiqc
diff --git a/modules/local/process/dupradar.nf b/modules/local/process/dupradar.nf
index 12fb53843..fd6bad99c 100644
--- a/modules/local/process/dupradar.nf
+++ b/modules/local/process/dupradar.nf
@@ -11,8 +11,12 @@ process DUPRADAR {
         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::bioconductor-dupradar=1.18.0" : null)
-    container "quay.io/biocontainers/bioconductor-dupradar:1.18.0--r40_1"
+    conda (params.enable_conda ? "bioconda::bioconductor-dupradar=1.18.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bioconductor-dupradar:1.18.0--r40_1"
+    } else {
+        container "quay.io/biocontainers/bioconductor-dupradar:1.18.0--r40_1"
+    }
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/process/get_chrom_sizes.nf b/modules/local/process/get_chrom_sizes.nf
index c7cfba489..1dbca7f7d 100644
--- a/modules/local/process/get_chrom_sizes.nf
+++ b/modules/local/process/get_chrom_sizes.nf
@@ -12,8 +12,12 @@ process GET_CHROM_SIZES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:"genome", publish_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:
     path fasta
diff --git a/modules/local/process/get_software_versions.nf b/modules/local/process/get_software_versions.nf
index 7ad040579..06a3ff649 100644
--- a/modules/local/process/get_software_versions.nf
+++ b/modules/local/process/get_software_versions.nf
@@ -11,8 +11,12 @@ process GET_SOFTWARE_VERSIONS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     cache false
 
diff --git a/modules/local/process/gffread.nf b/modules/local/process/gffread.nf
index a01692fa8..7897b60c6 100644
--- a/modules/local/process/gffread.nf
+++ b/modules/local/process/gffread.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 fasta
diff --git a/modules/local/process/gtf2bed.nf b/modules/local/process/gtf2bed.nf
index 2bf1225ac..3b067be2a 100644
--- a/modules/local/process/gtf2bed.nf
+++ b/modules/local/process/gtf2bed.nf
@@ -13,8 +13,12 @@ process GTF2BED {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
-    container "quay.io/biocontainers/perl:5.26.2"
+    conda (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/perl:5.26.2"
+    } else {
+        container "quay.io/biocontainers/perl:5.26.2"
+    }
 
     input:
     path gtf
diff --git a/modules/local/process/gtf_gene_filter.nf b/modules/local/process/gtf_gene_filter.nf
index e8ff65dfd..ba57f6c1c 100644
--- a/modules/local/process/gtf_gene_filter.nf
+++ b/modules/local/process/gtf_gene_filter.nf
@@ -9,8 +9,12 @@ process GTF_GENE_FILTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     input:
     path fasta
diff --git a/modules/local/process/gunzip.nf b/modules/local/process/gunzip.nf
index 1256895c1..c0f404364 100644
--- a/modules/local/process/gunzip.nf
+++ b/modules/local/process/gunzip.nf
@@ -10,8 +10,12 @@ process GUNZIP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     path archive
@@ -24,7 +28,7 @@ process GUNZIP {
     def software = getSoftwareName(task.process)
     gunzip       = archive.toString() - '.gz'
     """
-    gunzip --force $options.args $archive
+    gunzip -f $options.args $archive
     echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//' > ${software}.version.txt
     """
 }
diff --git a/modules/local/process/multiqc.nf b/modules/local/process/multiqc.nf
index d7b2af282..b39c346be 100644
--- a/modules/local/process/multiqc.nf
+++ b/modules/local/process/multiqc.nf
@@ -10,8 +10,12 @@ process MULTIQC {
         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::multiqc=1.9" : null)
-    container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
+    conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0"
+    } else {
+        container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
+    }
 
     input:
     path multiqc_config
diff --git a/modules/local/process/multiqc_custom_biotype.nf b/modules/local/process/multiqc_custom_biotype.nf
index 88cd0dfad..22f1fac9d 100644
--- a/modules/local/process/multiqc_custom_biotype.nf
+++ b/modules/local/process/multiqc_custom_biotype.nf
@@ -10,8 +10,12 @@ process MULTIQC_CUSTOM_BIOTYPE {
         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 ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     input:
     tuple val(meta), path(count)
diff --git a/modules/local/process/multiqc_custom_fail_mapped.nf b/modules/local/process/multiqc_custom_fail_mapped.nf
index 1278bca3a..7ed3ad7bd 100644
--- a/modules/local/process/multiqc_custom_fail_mapped.nf
+++ b/modules/local/process/multiqc_custom_fail_mapped.nf
@@ -8,8 +8,12 @@ process MULTIQC_CUSTOM_FAIL_MAPPED {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     val fail_mapped
diff --git a/modules/local/process/multiqc_custom_strand_check.nf b/modules/local/process/multiqc_custom_strand_check.nf
index b2bd6461b..e85f7952c 100644
--- a/modules/local/process/multiqc_custom_strand_check.nf
+++ b/modules/local/process/multiqc_custom_strand_check.nf
@@ -8,8 +8,12 @@ process MULTIQC_CUSTOM_STRAND_CHECK {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     val fail_strand
diff --git a/modules/local/process/rsem_merge_counts.nf b/modules/local/process/rsem_merge_counts.nf
index d5af9aec1..e5cfd2f74 100644
--- a/modules/local/process/rsem_merge_counts.nf
+++ b/modules/local/process/rsem_merge_counts.nf
@@ -9,8 +9,12 @@ process RSEM_MERGE_COUNTS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     path ('genes/*')
diff --git a/modules/local/process/salmon_merge_counts.nf b/modules/local/process/salmon_merge_counts.nf
index 5b2e09319..7a31b35c0 100644
--- a/modules/local/process/salmon_merge_counts.nf
+++ b/modules/local/process/salmon_merge_counts.nf
@@ -9,8 +9,12 @@ process SALMON_MERGE_COUNTS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     path ('genes_counts/*')
diff --git a/modules/local/process/salmon_summarizedexperiment.nf b/modules/local/process/salmon_summarizedexperiment.nf
index 98506f666..9ca904ead 100644
--- a/modules/local/process/salmon_summarizedexperiment.nf
+++ b/modules/local/process/salmon_summarizedexperiment.nf
@@ -10,9 +10,13 @@ process SALMON_SUMMARIZEDEXPERIMENT {
         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::bioconductor-summarizedexperiment=1.18.1" : null)
-    container "quay.io/biocontainers/bioconductor-summarizedexperiment:1.18.1--r40_0"
-
+    conda (params.enable_conda ? "bioconda::bioconductor-summarizedexperiment=1.18.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.18.1--r40_0"
+    } else {
+        container "quay.io/biocontainers/bioconductor-summarizedexperiment:1.18.1--r40_0"
+    }
+    
     input:
     path counts
     path tpm
diff --git a/modules/local/process/salmon_tx2gene.nf b/modules/local/process/salmon_tx2gene.nf
index 45979e54e..7c8276e06 100644
--- a/modules/local/process/salmon_tx2gene.nf
+++ b/modules/local/process/salmon_tx2gene.nf
@@ -10,8 +10,12 @@ process SALMON_TX2GENE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     input:
     path ("salmon/*")
diff --git a/modules/local/process/salmon_tximport.nf b/modules/local/process/salmon_tximport.nf
index 162457288..37525b886 100644
--- a/modules/local/process/salmon_tximport.nf
+++ b/modules/local/process/salmon_tximport.nf
@@ -10,8 +10,12 @@ process SALMON_TXIMPORT {
         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::bioconductor-tximeta=1.6.3" : null)
-    container "quay.io/biocontainers/bioconductor-tximeta:1.6.3--r40_0"
+    conda (params.enable_conda ? "bioconda::bioconductor-tximeta=1.6.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bioconductor-tximeta:1.6.3--r40_0"
+    } else {
+        container "quay.io/biocontainers/bioconductor-tximeta:1.6.3--r40_0"
+    }
     
     input:
     tuple val(meta), path("salmon/*")
diff --git a/modules/local/process/samplesheet_check.nf b/modules/local/process/samplesheet_check.nf
index 869739afe..ae025ef56 100644
--- a/modules/local/process/samplesheet_check.nf
+++ b/modules/local/process/samplesheet_check.nf
@@ -12,8 +12,12 @@ process SAMPLESHEET_CHECK {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     input:
     path samplesheet
diff --git a/modules/local/process/sra_fastq_ftp.nf b/modules/local/process/sra_fastq_ftp.nf
index 803e725c2..6a80a549e 100644
--- a/modules/local/process/sra_fastq_ftp.nf
+++ b/modules/local/process/sra_fastq_ftp.nf
@@ -14,8 +14,12 @@ process SRA_FASTQ_FTP {
         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 ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     tuple val(meta), val(fastq)
diff --git a/modules/local/process/sra_ids_to_runinfo.nf b/modules/local/process/sra_ids_to_runinfo.nf
index b75332c7e..63ca2fe91 100644
--- a/modules/local/process/sra_ids_to_runinfo.nf
+++ b/modules/local/process/sra_ids_to_runinfo.nf
@@ -13,8 +13,12 @@ process SRA_IDS_TO_RUNINFO {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
     
     input:
     val id
diff --git a/modules/local/process/sra_merge_samplesheet.nf b/modules/local/process/sra_merge_samplesheet.nf
index b2db81f10..f8e87a271 100644
--- a/modules/local/process/sra_merge_samplesheet.nf
+++ b/modules/local/process/sra_merge_samplesheet.nf
@@ -11,8 +11,12 @@ process SRA_MERGE_SAMPLESHEET {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
 
     input:
     path ('samplesheets/*')
diff --git a/modules/local/process/sra_runinfo_to_ftp.nf b/modules/local/process/sra_runinfo_to_ftp.nf
index 48bce5bca..e8dd52a40 100644
--- a/modules/local/process/sra_runinfo_to_ftp.nf
+++ b/modules/local/process/sra_runinfo_to_ftp.nf
@@ -11,9 +11,13 @@ process SRA_RUNINFO_TO_FTP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
-    
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
+        
     input:
     path runinfo
     
diff --git a/modules/local/process/untar.nf b/modules/local/process/untar.nf
index e9b00fe6b..5878edb1a 100644
--- a/modules/local/process/untar.nf
+++ b/modules/local/process/untar.nf
@@ -10,9 +10,13 @@ process UNTAR {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "biocontainers/biocontainers:v1.2.0_cv1"
-    
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
     input:
     path archive
     
diff --git a/modules/nf-core/software/fastqc/main.nf b/modules/nf-core/software/fastqc/main.nf
index 3edc97a14..3cb510ac7 100644
--- a/modules/nf-core/software/fastqc/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/gffread/main.nf b/modules/nf-core/software/gffread/main.nf
index 9906f6206..0e446ac86 100644
--- a/modules/nf-core/software/gffread/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/hisat2/align/main.nf b/modules/nf-core/software/hisat2/align/main.nf
index d2c6fbcd6..ef37b7b78 100644
--- a/modules/nf-core/software/hisat2/align/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/hisat2/build/main.nf b/modules/nf-core/software/hisat2/build/main.nf
index 25596c892..5d83118c8 100644
--- a/modules/nf-core/software/hisat2/build/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/hisat2/extractsplicesites/main.nf b/modules/nf-core/software/hisat2/extractsplicesites/main.nf
index bfd2cf389..665f47031 100644
--- a/modules/nf-core/software/hisat2/extractsplicesites/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/picard/markduplicates/main.nf b/modules/nf-core/software/picard/markduplicates/main.nf
index 032a40706..84dc3d653 100644
--- a/modules/nf-core/software/picard/markduplicates/main.nf
+++ b/modules/nf-core/software/picard/markduplicates/main.nf
@@ -11,9 +11,13 @@ 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)
-    container "quay.io/biocontainers/picard:2.23.8--0"    
-
+    conda (params.enable_conda ? "bioconda::picard=2.23.8" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0"
+    } else {
+        container "quay.io/biocontainers/picard:2.23.8--0"
+    }
+    
     input:
     tuple val(meta), path(bam)
     
diff --git a/modules/nf-core/software/preseq/lcextrap/main.nf b/modules/nf-core/software/preseq/lcextrap/main.nf
index 89afeda7b..56645274a 100644
--- a/modules/nf-core/software/preseq/lcextrap/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/qualimap/rnaseq/main.nf b/modules/nf-core/software/qualimap/rnaseq/main.nf
index f24001e84..adbc7865f 100644
--- a/modules/nf-core/software/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rsem/calculateexpression/main.nf b/modules/nf-core/software/rsem/calculateexpression/main.nf
index f00d76868..478670d06 100644
--- a/modules/nf-core/software/rsem/calculateexpression/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rsem/preparereference/main.nf b/modules/nf-core/software/rsem/preparereference/main.nf
index 982f6cdda..3aceed8cf 100644
--- a/modules/nf-core/software/rsem/preparereference/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/bamstat/main.nf b/modules/nf-core/software/rseqc/bamstat/main.nf
index e9a34add9..f6525cd09 100644
--- a/modules/nf-core/software/rseqc/bamstat/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/inferexperiment/main.nf b/modules/nf-core/software/rseqc/inferexperiment/main.nf
index 79dfd4f9c..4f35d3e3b 100644
--- a/modules/nf-core/software/rseqc/inferexperiment/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/innerdistance/main.nf b/modules/nf-core/software/rseqc/innerdistance/main.nf
index 9ace426d7..8273b3536 100644
--- a/modules/nf-core/software/rseqc/innerdistance/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/junctionannotation/main.nf b/modules/nf-core/software/rseqc/junctionannotation/main.nf
index 9cc6d00fa..a12782f0e 100644
--- a/modules/nf-core/software/rseqc/junctionannotation/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/junctionsaturation/main.nf b/modules/nf-core/software/rseqc/junctionsaturation/main.nf
index a472aba5d..e607c8228 100644
--- a/modules/nf-core/software/rseqc/junctionsaturation/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/readdistribution/main.nf b/modules/nf-core/software/rseqc/readdistribution/main.nf
index de99185fa..b248fc651 100644
--- a/modules/nf-core/software/rseqc/readdistribution/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/rseqc/readduplication/main.nf b/modules/nf-core/software/rseqc/readduplication/main.nf
index 4a3998da7..23bc602c7 100644
--- a/modules/nf-core/software/rseqc/readduplication/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/salmon/index/main.nf b/modules/nf-core/software/salmon/index/main.nf
index 341857a44..48a4506b6 100644
--- a/modules/nf-core/software/salmon/index/main.nf
+++ b/modules/nf-core/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=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
+        container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    }
 
     input:
     path genome_fasta
diff --git a/modules/nf-core/software/salmon/quant/main.nf b/modules/nf-core/software/salmon/quant/main.nf
index bb0d07d94..4a4a9eac1 100644
--- a/modules/nf-core/software/salmon/quant/main.nf
+++ b/modules/nf-core/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=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
+        container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    }
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/software/samtools/flagstat/main.nf b/modules/nf-core/software/samtools/flagstat/main.nf
index 46e95df06..e23f0864f 100644
--- a/modules/nf-core/software/samtools/flagstat/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/samtools/idxstats/main.nf b/modules/nf-core/software/samtools/idxstats/main.nf
index 29e680df4..40ac4702d 100644
--- a/modules/nf-core/software/samtools/idxstats/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/samtools/index/main.nf b/modules/nf-core/software/samtools/index/main.nf
index 23c9ec418..c0dadfd59 100644
--- a/modules/nf-core/software/samtools/index/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/samtools/sort/main.nf b/modules/nf-core/software/samtools/sort/main.nf
index a872e11f2..e43e4a9bb 100644
--- a/modules/nf-core/software/samtools/sort/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/samtools/stats/main.nf b/modules/nf-core/software/samtools/stats/main.nf
index e1949ee70..ba38c6ad3 100644
--- a/modules/nf-core/software/samtools/stats/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/sortmerna/main.nf b/modules/nf-core/software/sortmerna/main.nf
index a1ea48645..5f2c34f99 100644
--- a/modules/nf-core/software/sortmerna/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/star/align/main.nf b/modules/nf-core/software/star/align/main.nf
index c143ba1df..866608d85 100644
--- a/modules/nf-core/software/star/align/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/star/genomegenerate/main.nf b/modules/nf-core/software/star/genomegenerate/main.nf
index 915b56752..e9aa12345 100644
--- a/modules/nf-core/software/star/genomegenerate/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/stringtie/main.nf b/modules/nf-core/software/stringtie/main.nf
index ba2c42bd8..35f5eab81 100644
--- a/modules/nf-core/software/stringtie/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/subread/featurecounts/main.nf b/modules/nf-core/software/subread/featurecounts/main.nf
index e8644af5c..55ad94b1f 100644
--- a/modules/nf-core/software/subread/featurecounts/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/trimgalore/main.nf b/modules/nf-core/software/trimgalore/main.nf
index 742ffaf53..79cc74562 100644
--- a/modules/nf-core/software/trimgalore/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/software/ucsc/bedgraphtobigwig/main.nf
index 873481cf6..4a8e95e90 100644
--- a/modules/nf-core/software/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/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/modules/nf-core/software/umitools/dedup/main.nf b/modules/nf-core/software/umitools/dedup/main.nf
index 8348cda4f..09eac7f76 100644
--- a/modules/nf-core/software/umitools/dedup/main.nf
+++ b/modules/nf-core/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=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
+        container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/software/umitools/extract/main.nf b/modules/nf-core/software/umitools/extract/main.nf
index d04f2e3dc..316fec22d 100644
--- a/modules/nf-core/software/umitools/extract/main.nf
+++ b/modules/nf-core/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=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
+        container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    }
 
     input:
     tuple val(meta), path(reads)
diff --git a/nextflow.config b/nextflow.config
index 447414b30..2d5856a06 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -90,6 +90,7 @@ params {
   igenomes_base              = 's3://ngi-igenomes/igenomes/'
   tracedir                   = "${params.outdir}/pipeline_info"
   igenomes_ignore            = false
+  singularity_pull_docker_container = false
 
   // Config options
   custom_config_version      = 'master'
@@ -182,8 +183,8 @@ manifest {
   homePage        = 'https://github.com/nf-core/rnaseq'
   description     = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
   mainScript      = 'main.nf'
-  nextflowVersion = '>=20.07.1'
-  version         = '2.1dev'
+  nextflowVersion = '!>=20.11.0-edge'
+  version         = '3.0'
 }
 
 // Function to ensure that resource requirements don't go beyond
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f52b3ae00..99a6a3e9e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -593,6 +593,13 @@
                     "fa_icon": "fas fa-network-wired",
                     "hidden": true
                 },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-toolbox",
+                    "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
+                },
                 "enable_conda": {
                     "type": "boolean",
                     "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",