From d75cb751119dce05534ae7c8321e7eeec98f5e05 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Thu, 17 Dec 2020 07:33:44 +0100
Subject: [PATCH] added singularity; edge NXF version

---
 .github/workflows/bowtie_align.yml | 10 +++++++---
 .github/workflows/bowtie_index.yml | 11 ++++++++---
 software/bowtie/align/main.nf      |  8 ++++++--
 software/bowtie/align/meta.yml     |  5 +++++
 software/bowtie/index/main.nf      |  9 ++++++---
 software/bowtie/index/meta.yml     |  5 +++++
 6 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml
index 796b3389..e3b645c8 100644
--- a/.github/workflows/bowtie_align.yml
+++ b/.github/workflows/bowtie_align.yml
@@ -16,16 +16,20 @@ on:
 jobs:
     ci_test:
         runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                nxf_version: [20.11.0-edge]
         env:
             NXF_ANSI_LOG: false
         steps:
             - uses: actions/checkout@v2
 
             - name: Install Nextflow
+              env:
+                NXF_VER: ${{ matrix.nxf_version }}
               run: |
-                  export NXF_VER="20.07.1"
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
+              wget -qO- get.nextflow.io | bash
+              sudo mv nextflow /usr/local/bin/
 
             - name: Set up Python
               uses: actions/setup-python@v2
diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml
index 80ff13c9..9f5aa8ac 100644
--- a/.github/workflows/bowtie_index.yml
+++ b/.github/workflows/bowtie_index.yml
@@ -14,16 +14,21 @@ on:
 jobs:
     ci_test:
         runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                nxf_version: [20.11.0-edge]
         env:
             NXF_ANSI_LOG: false
         steps:
             - uses: actions/checkout@v2
 
             - name: Install Nextflow
+              env:
+                NXF_VER: ${{ matrix.nxf_version }}
               run: |
-                  export NXF_VER="20.07.1"
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
+              wget -qO- get.nextflow.io | bash
+              sudo mv nextflow /usr/local/bin/
+
 
             - name: Set up Python
               uses: actions/setup-python@v2
diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 6a7ea8d8..58906d61 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -11,8 +11,12 @@ process BOWTIE_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::bowtie=1.3.0 bioconda::samtools=1.10" : null)
-    container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+    }
 
     input:
     tuple val(meta), path(reads)
diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml
index fc18a2c9..633ef56a 100644
--- a/software/bowtie/align/meta.yml
+++ b/software/bowtie/align/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.
     - save_unaligned:
         type: boolean
         description: Save unaligned reads
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 5a0e18e5..1a3801b6 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -11,9 +11,12 @@ process BOWTIE_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::bowtie=1.3.0" : null)
-    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
-    
+    conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1"
+    } else {
+        container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+    }
 
     input:
     path fasta
diff --git a/software/bowtie/index/meta.yml b/software/bowtie/index/meta.yml
index 0a8c23f7..db781a0a 100644
--- a/software/bowtie/index/meta.yml
+++ b/software/bowtie/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