Update all other modules

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"

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) 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
-    container "biocontainers/bwa:v0.7.17_cv1"
+    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
     

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)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
-    container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    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)
     

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)
+    conda (params.enable_conda ? "bioconda::homer=4.11" : null)
-    container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
-    container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
+    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)

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)
+    conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
-    container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
+    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

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)
+    conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
-    container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
+    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)
     

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

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