Merge pull request #109 from drpatelh/singularity

Bump NF version and add direct download Singularity paths back in to modules
2024-12-31 03:32:10 -05:00 · 2020-12-14 12:20:03 +00:00 · 2020-12-14 12:20:03 +00:00 · ceef4a6044
commit ceef4a6044
parent 5561fb58d8 141ca290b7
76 changed files with 374 additions and 121 deletions
--- a/.github/workflows/bwa_index.yml
+++ b/.github/workflows/bwa_index.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/bwa_mem.yml
+++ b/.github/workflows/bwa_mem.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/fastqc.yml
+++ b/.github/workflows/fastqc.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/multiqc.yml
+++ b/.github/workflows/multiqc.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/picard_collectmultiplemetrics.yml
+++ b/.github/workflows/picard_collectmultiplemetrics.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/picard_markduplicates.yml
+++ b/.github/workflows/picard_markduplicates.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/picard_mergesamfiles.yml
+++ b/.github/workflows/picard_mergesamfiles.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/samtools_flagstat.yml
+++ b/.github/workflows/samtools_flagstat.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/samtools_idxstats.yml
+++ b/.github/workflows/samtools_idxstats.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/samtools_index.yml
+++ b/.github/workflows/samtools_index.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/samtools_sort.yml
+++ b/.github/workflows/samtools_sort.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/samtools_stats.yml
+++ b/.github/workflows/samtools_stats.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/.github/workflows/trimgalore.yml
+++ b/.github/workflows/trimgalore.yml
@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        nxf_version: [20.07.1, ""]
+        nxf_version: [20.11.0-edge]
    env:
      NXF_ANSI_LOG: false
    steps:
--- a/README.md
+++ b/README.md
@ -1,6 +1,6 @@
 # ![nf-core/modules](docs/images/nfcore-modules_logo.png)

-[![Nextflow](https://img.shields.io/badge/nextflow-DSL2-23aa62.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/)
--- a/deprecated/lib/checksum.groovy
+++ b/deprecated/lib/checksum.groovy
--- a/software/SOFTWARE/TOOL/main.nf
+++ b/software/SOFTWARE/TOOL/main.nf
@ -39,13 +39,17 @@ process SOFTWARE_TOOL {
    // TODO nf-core: List required Conda packages.
    //               Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below.
    //               Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement.
-    conda     (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)

    // TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools
    //               Click on the Pacakages and Containers tab, sort by Version and get the portion of the link after the docker pull command where Type is Docker.
    //               You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently.
    //               If required, multi-tool containers may also be available and are usually named to start with "mulled".
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    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:
    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
--- a/software/SOFTWARE/TOOL/meta.yml
+++ b/software/SOFTWARE/TOOL/meta.yml
@ -37,6 +37,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 ## TODO nf-core: Add a description of all of the variables used as input
 input:
    - meta:
--- a/software/bwa/index/main.nf
+++ b/software/bwa/index/main.nf
@ -11,9 +11,13 @@ process BWA_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::bwa=0.7.17" : null) 
-    container "biocontainers/bwa:v0.7.17_cv1"
-    
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
+    } else {
+        container "biocontainers/bwa:v0.7.17_cv1"
+    }
+
    input:
    path fasta
    
--- a/software/bwa/index/meta.yml
+++ b/software/bwa/index/meta.yml
@ -29,6 +29,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - fasta:
        type: file
--- a/software/bwa/mem/main.nf
+++ b/software/bwa/mem/main.nf
@ -11,8 +11,12 @@ process BWA_MEM {
        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::bwa=0.7.17 bioconda::samtools=1.10" : null)
-    container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    }
    
    input:
    tuple val(meta), path(reads)
--- a/software/bwa/mem/meta.yml
+++ b/software/bwa/mem/meta.yml
@ -32,6 +32,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- a/software/deeptools/computematrix/main.nf
+++ b/software/deeptools/computematrix/main.nf
@ -11,8 +11,12 @@ process DEEPTOOLS_COMPUTEMATRIX {
        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::deeptools=3.4.3" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+    } else {
+        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+    }

    input:
    tuple val(meta), path(bigwig)
--- a/software/deeptools/plotfingerprint/main.nf
+++ b/software/deeptools/plotfingerprint/main.nf
@ -11,8 +11,12 @@ process DEEPTOOLS_PLOTFINGERPRINT {
        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::deeptools=3.4.3" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+    } else {
+        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+    }

    input:
    tuple val(meta), path(bams), path(bais)
--- a/software/deeptools/plotheatmap/main.nf
+++ b/software/deeptools/plotheatmap/main.nf
@ -11,8 +11,12 @@ process DEEPTOOLS_PLOTHEATMAP {
        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::deeptools=3.4.3" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+    } else {
+        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+    }

    input:
    tuple val(meta), path(matrix)
--- a/software/deeptools/plotprofile/main.nf
+++ b/software/deeptools/plotprofile/main.nf
@ -11,9 +11,13 @@ process DEEPTOOLS_PLOTPROFILE {
        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::deeptools=3.4.3" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
-    
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+    } else {
+        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+    }
+
    input:
    tuple val(meta), path(matrix)
    
--- 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)
--- a/software/fastqc/meta.yml
+++ b/software/fastqc/meta.yml
@ -31,6 +31,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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
--- 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
--- 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
--- 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

--- a/software/homer/annotatepeaks/main.nf
+++ b/software/homer/annotatepeaks/main.nf
@ -13,8 +13,12 @@ process HOMER_ANNOTATEPEAKS {
        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::homer=4.11" : null)
-    container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
+    conda (params.enable_conda ? "bioconda::homer=4.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
+    } else {
+        container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
+    }

    input:
    tuple val(meta), path(peak)
--- a/software/macs2/callpeak/main.nf
+++ b/software/macs2/callpeak/main.nf
@ -11,8 +11,12 @@ process MACS2_CALLPEAK {
        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::macs2=2.2.7.1" : null)
-    container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
+    conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
+    } else {
+        container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1"
+    }

    input:
    tuple val(meta), path(ipbam), path(controlbam)
--- a/software/multiqc/main.nf
+++ b/software/multiqc/main.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_files
--- a/software/multiqc/meta.yml
+++ b/software/multiqc/meta.yml
@ -27,6 +27,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - multiqc_files:
        type: file
--- a/software/phantompeakqualtools/main.nf
+++ b/software/phantompeakqualtools/main.nf
@ -13,9 +13,13 @@ process PHANTOMPEAKQUALTOOLS {
        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::phantompeakqualtools=1.2.2" : null)
-    container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
-
+    conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
+    } else {
+        container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
+    }
+    
    input:
    tuple val(meta), path(bam)
    
--- a/software/picard/collectmultiplemetrics/main.nf
+++ b/software/picard/collectmultiplemetrics/main.nf
@ -11,8 +11,12 @@ process PICARD_COLLECTMULTIPLEMETRICS {
        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)
--- a/software/picard/collectmultiplemetrics/meta.yml
+++ b/software/picard/collectmultiplemetrics/meta.yml
@ -30,6 +30,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
--- a/software/picard/markduplicates/meta.yml
+++ b/software/picard/markduplicates/meta.yml
@ -30,6 +30,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- a/software/picard/mergesamfiles/main.nf
+++ b/software/picard/mergesamfiles/main.nf
@ -11,8 +11,12 @@ process PICARD_MERGESAMFILES {
        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(bams)
--- a/software/picard/mergesamfiles/meta.yml
+++ b/software/picard/mergesamfiles/meta.yml
@ -28,6 +28,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
    
--- 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)
--- 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)
--- 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
--- 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)
--- 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)
--- 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)
--- 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)
--- 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)
--- 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)
--- 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)
--- 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
    """
-}
+}
--- 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)
--- 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)
--- a/software/samtools/flagstat/meta.yml
+++ b/software/samtools/flagstat/meta.yml
@ -32,6 +32,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
--- a/software/samtools/idxstats/meta.yml
+++ b/software/samtools/idxstats/meta.yml
@ -33,6 +33,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
--- a/software/samtools/index/meta.yml
+++ b/software/samtools/index/meta.yml
@ -30,6 +30,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
--- a/software/samtools/sort/meta.yml
+++ b/software/samtools/sort/meta.yml
@ -30,6 +30,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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)
    
--- a/software/samtools/stats/meta.yml
+++ b/software/samtools/stats/meta.yml
@ -31,6 +31,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
 input:
    - meta:
        type: map
--- 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
--- 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)
--- 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
--- 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)
--- 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)
--- 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)
--- a/software/trimgalore/meta.yml
+++ b/software/trimgalore/meta.yml
@ -29,6 +29,11 @@ params:
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
+    - 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.
    - clip_r1:
        type: integer
        description: |
--- 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
--- 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)
--- 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)
--- a/tests/software/picard/test.yml
+++ b/tests/software/picard/test.yml
@ -32,7 +32,7 @@
  files:
    - path: output/picard/test.MarkDuplicates.metrics.txt
    - path: output/picard/test.bam
-      md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
+      md5sum: 0ed0bfc94069380334ccd595f6d8207c

 - name: Run picard MarkDuplicates without a sorted bam file so it fails
  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config