Add --singularity_pull_docker_container to module yml

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:

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

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

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

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

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

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

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

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

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

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

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

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

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: |