Add support for apptainer containers

.gitignore

@@ -14,3 +14,4 @@ Validation_notes.md
 .Rproj.user
 */__pycache__/*.pyc
 assets/genoflu/GenoFLU
+*sif

environments/base.def

@@ -0,0 +1,43 @@
+BootStrap: docker
+From: python:3.9-slim
+
+%files
+    environment.yml /opt/environment.yml
+
+%post
+    # Install system dependencies
+    apt-get update && apt-get install -y \
+        wget \
+        bzip2 \
+        procps \
+        ca-certificates \
+        git \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/*
+
+    # Install Miniforge
+    wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash Miniforge3-Linux-x86_64.sh -b -f -p /opt/mamba && \
+    rm Miniforge3-Linux-x86_64.sh
+
+    # Add conda to PATH
+    . /opt/mamba/bin/activate
+
+    # Initialize mamba	
+    mamba init
+    . /root/.bashrc
+
+    # Create conda environment
+    mamba env create -f /opt/environment.yml
+
+    # Clean up
+    mamba clean -afy
+
+
+%environment
+	. /root/.bashrc && \
+    export CONDA_ENV_NAME=$(head -n1 /opt/environment.yml | cut -d' ' -f2)  && \
+    mamba activate $CONDA_ENV_NAME
+
+%runscript
+    exec "$@"

environments/fluviewer.def

@@ -0,0 +1,41 @@
+BootStrap: docker
+From: python:3.9-slim
+
+%files
+    fluviewer.yml /opt/environment.yml
+
+%post
+    # Install system dependencies
+    apt-get update && apt-get install -y \
+        wget \
+        bzip2 \
+        procps \
+        ca-certificates \
+        git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+    # Install Miniforge
+    wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash Miniforge3-Linux-x86_64.sh -b -f -p /opt/mamba && \
+    rm Miniforge3-Linux-x86_64.sh
+
+    # Add conda to PATH
+    . /opt/mamba/bin/activate && \
+    mamba init && \
+    . /root/.bashrc
+
+    # Create conda environment
+    mamba env create -f /opt/environment.yml
+
+    # Clean up
+    mamba clean -afy
+
+
+%environment
+	. /root/.bashrc && \
+    export CONDA_ENV_NAME=$(head -n1 /opt/environment.yml | cut -d' ' -f2)  && \
+    mamba activate $CONDA_ENV_NAME
+
+%runscript
+    exec "$@"

environments/nextclade.def

@@ -0,0 +1,41 @@
+BootStrap: docker
+From: python:3.9-slim
+
+%files
+    nextclade.yml /opt/environment.yml
+
+%post
+    # Install system dependencies
+    apt-get update && apt-get install -y \
+        wget \
+        bzip2 \
+        procps \
+        ca-certificates \
+        git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+    # Install Miniforge
+    wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash Miniforge3-Linux-x86_64.sh -b -f -p /opt/mamba && \
+    rm Miniforge3-Linux-x86_64.sh
+
+    # Add conda to PATH
+    . /opt/mamba/bin/activate && \
+    mamba init && \
+    . /root/.bashrc
+
+    # Create conda environment
+    mamba env create -f /opt/environment.yml
+
+    # Clean up
+    mamba clean -afy
+
+
+%environment
+	. /root/.bashrc && \
+    export CONDA_ENV_NAME=$(head -n1 /opt/environment.yml | cut -d' ' -f2)  && \
+    mamba activate $CONDA_ENV_NAME
+
+%runscript
+    exec "$@"

main.nf

@@ -55,7 +55,7 @@ workflow {
 
     ch_pipeline_provenance = pipeline_provenance(ch_workflow_metadata)
 
-    ch_primers = Channel.fromPath(params.primer_path)
+    ch_primers = Channel.fromPath(params.primers)
 
     ch_db = Channel.fromPath(params.db)
 

nextflow.config

@@ -1,10 +1,10 @@
 manifest {
-  author = 'James Zlosnik (nextflow pipeline)/Kevin Kuchinski (FluViewer)'
-  name = 'BCCDC-PHL/fluviewer-nf'
-  version = '0.3.0'
-  description = 'BCCDC-PHL FluViewer'
-  mainScript = 'main.nf'
-  nextflowVersion = '>=20.01.0'
+    author = 'James Zlosnik (nextflow pipeline)/Kevin Kuchinski (FluViewer)'
+    name = 'BCCDC-PHL/fluviewer-nf'
+    version = '0.3.0'
+    description = 'BCCDC-PHL FluViewer'
+    mainScript = 'main.nf'
+    nextflowVersion = '>=20.01.0'
 }
 
 params {
@@ -17,7 +17,7 @@ params {
     fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
     fastq_search_path = makeFastqSearchPath( illumina_suffixes, fastq_exts )
     primer_path = "${baseDir}/assets/"
-    primers = "${baseDir}/assets/primers.fa"
+    primers = "${projectDir}/assets/primers.fa"
     rev_primers = "${baseDir}/assets/primers_rev_comp.fa"
     pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
     pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
@@ -51,7 +51,7 @@ def makeFastqSearchPath ( illumina_suffixes, fastq_exts ) {
 def parseRunName ( fastq_input ) {
     run_name = (params.fastq_input =~ /([^\/]+)\/?$/)[0][1]
     if (!run_name) {                                                         
-      throw new RuntimeException("ERROR: Parsing run name from FASTQ path failed.")
+        throw new RuntimeException("ERROR: Parsing run name from FASTQ path failed.")
     }
     return run_name
 }
@@ -69,33 +69,48 @@ def parsePipelineName(name) {
 
 profiles {
     conda {
-	conda.enabled = true
-	process.conda = "$baseDir/environments/environment.yml"
-	if (params.cache) {
-	    conda.cacheDir = params.cache
-	}
-	conda.useMamba = true
+        conda.enabled = true
+        process.conda = "$baseDir/environments/environment.yml"
+        if (params.cache) {
+            conda.cacheDir = params.cache
+        }
+        conda.useMamba = true
+    }
+
+    apptainer {
+        apptainer.enabled = true
     }
 }
 
+
+trace.overwrite = true
+report.overwrite = true 
+timeline.overwrite = true
+
 process {
+    container = "${projectDir}/environments/base.sif"
+
     withName: normalize_depth {
-	conda = "$baseDir/environments/fluviewer.yml"
-	memory = '50 GB'
+        conda = "${projectDir}/environments/fluviewer.yml"
+        container = "${projectDir}/environments/fluviewer.sif"
+        memory = '50 GB'
+        cpus = 4
     }
 
     withName: fluviewer {
-	conda = "$baseDir/environments/fluviewer.yml"
-	cpus = 8
+        conda = "${projectDir}/environments/fluviewer.yml"
+        container = "${projectDir}/environments/fluviewer.sif"
+        cpus = 8
     }
 
     withName: cutadapt {
-	cpus = 8
+        cpus = 8
     }
 
     withName: clade_calling {
-	conda = "$baseDir/environments/nextclade.yml"
-	cpus = 4
+        conda = "${projectDir}/environments/nextclade.yml"
+        container = "${projectDir}/environments/nextclade.sif"
+        cpus = 4
     }
 }