Merge pull request #3 from rki-mf1/feature/docker

Feature/docker
rki-mf1 · Feb 19, 2025 · 34e251a · 34e251a
2 parents ecb519c + 924c26c
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diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,9 @@ results/
 conda/
 .conda/
 
+# Singularity
+singularity/
+
 # nextflow
 .nextflow/
 .nextflow.log*

diff --git a/README.md b/README.md
@@ -5,6 +5,11 @@
 <h3 align="center"> Mutation-Based Early Warning System to Prioritize Concerning Influenza Variants from Sequencing Data </h3>
 </div>
 
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![run with conda](https://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/)
+
 The goal of VirusWarn-Flu is to detect concerning Influenza variants from sequencing data.
 It does so by parsing Influenza genomes and detecting amino acids mutations in the spike proteins that can be associated with a phenotypic change. The phenotypic changes are annotated according to the knowledge accumulated on previous variants. 
 The tool is based on <a href="https://github.com/rki-mf1/VirusWarn-SC2"><strong>VirusWarn-SC2</strong></a>, which was invented for SARS-CoV-2.
@@ -23,16 +28,24 @@ VirusWarn-Flu is part of *VirusWarn*
 
 ## Quick Installation
 
-To run the pipeline, you need to have `conda` and `Nextflow` installed and set up.
-All other dependencies will be installed over `conda` in the pipeline.
+To run the pipeline, you need to have `Nextflow` and either `conda`, `Docker` or `Singularity`.
+
+<details><summary><strong>Click!</strong> If you want to install <code>Nextflow</code> directly, you can use the following one-liner. </summary>
+
+```bash
+wget -qO- https://get.nextflow.io | bash
+```
+</details>
+
+<details><summary><strong>Click!</strong> If you want to set up <code>conda</code> to run the pipeline and install all other dependencies through it, you can use the following steps. </summary>
 
-To install `conda`, use the following bash commands if you are working on **Linux**:
+Use the following bash commands if you are working on **Linux**:
 ```bash
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh
 ```
 
-To install `conda`, use the following bash commands if you are working on **Mac**:
+Use the following bash commands if you are working on **Mac**:
 ```bash
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh
 bash Miniconda3-latest-MacOSX-arm64.sh
@@ -43,31 +56,53 @@ Then, `Nextflow` an be installed over `conda`:
 conda create -n nextflow -c bioconda nextflow
 conda activate nextflow
 ```
+</details>
+
+### Get / Update VirusWarn-Flu
 
-The VirusWarn-Flu repository can be cloned from Git:
 ```bash
-git clone https://github.com/rki-mf1/VirusWarn-Flu.git
+nextflow pull rki-mf1/VirusWarn-Flu
 ```
 
 ### Call help
 
 ```bash
-nextflow run main.nf --help
+nextflow run rki-mf1/VirusWarn-Flu -r <version> --help
 ```
 
 ## Running VirusWarn-Flu
 
+With a `conda`, please run:
+
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_h1n1.fasta' \
      --metadata 'test/metadata_h1n1.xlsx'
 ```
 
+With a `Docker`, please run:
+
+```bash
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
+     -profile docker,local \
+     --fasta 'test/openflu_h1n1.fasta' \
+     --metadata 'test/metadata_h1n1.xlsx'
+```
+
+With a `Singularity`, please run:
+
+```bash
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
+     -profile singularity,local \
+     --fasta 'test/openflu_h1n1.fasta' \
+     --metadata 'test/metadata_h1n1.xlsx'
+```
+
 ### Running VirusWarn-Flu with splitting (Input from OpenFlu)
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_combi.fasta' \
      --metadata 'test/metadata_combi.xlsx' \

diff --git a/config/conda.config b/config/conda.config
@@ -1,7 +1,6 @@
 process {
-    withLabel: split        {   conda = "$projectDir/envs/split.yml"        }
-    withLabel: qc           {   conda = "$projectDir/envs/qc.yml"           }
+    withLabel: biopython    {   conda = "$projectDir/envs/biopython.yml"    }
     withLabel: nextclade    {   conda = "$projectDir/envs/nextclade.yml"    }
-    withLabel: annotation   {   conda = "$projectDir/envs/annotation.yml"   }
+    withLabel: qc           {   conda = "$projectDir/envs/qc.yml"           }
     withLabel: report       {   conda = "$projectDir/envs/report.yml"       }
 }
diff --git a/config/container.config b/config/container.config
@@ -0,0 +1,6 @@
+process {
+    withLabel: biopython    {   container = "rkimf1/viruswarn-biopython:1.79--6875bf5"        }
+    withLabel: nextclade    {   container = "rkimf1/viruswarn-flu-nextclade:3.0.1--32ead72"   }
+    withLabel: qc           {   container = "rkimf1/viruswarn-flu-qc:2.25--f0db0b4"           }
+    withLabel: report       {   container = "rkimf1/viruswarn-flu-report:2.25--782b9d7"       }
+}
diff --git a/envs/annotation.yml → envs/biopython.yml b/envs/annotation.yml → envs/biopython.yml
@@ -1,8 +1,7 @@
-name: annotation
+name: biopython
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python=3.9.7
   - biopython=1.79

diff --git a/envs/nextclade.yml b/envs/nextclade.yml
@@ -2,7 +2,6 @@ name: nextclade
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - nextclade=3.0.1
   - python=3.9.7

diff --git a/envs/qc.yml b/envs/qc.yml
@@ -2,7 +2,7 @@ name: qc
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - r
 dependencies:
   - python=3.9.7
   - pandas=1.5.3

diff --git a/envs/report.yml b/envs/report.yml
@@ -3,7 +3,6 @@ channels:
   - conda-forge
   - bioconda
   - r
-  - defaults
 dependencies:
   - r-base=4.3.2
   - r-optparse=1.7.3

diff --git a/envs/split.yml b/envs/split.yml
diff --git a/modules/local/annotation.nf b/modules/local/annotation.nf
@@ -1,5 +1,5 @@
 process ANNOTATION {
-    label 'annotation'
+    label 'biopython'
 
     publishDir "${params.output}/${params.annot_dir}", mode: params.publish_dir_mode
 

diff --git a/modules/local/split.nf b/modules/local/split.nf
@@ -1,5 +1,5 @@
 process SPLIT {
-    label 'split'
+    label 'biopython'
 
     publishDir "${params.output}/${params.split_dir}", mode: params.publish_dir_mode
 

diff --git a/nextflow.config b/nextflow.config
@@ -52,6 +52,7 @@ params {
 
     // location for engines' cache
     conda_cache_dir = 'conda'
+    singularity_cache_dir = 'singularity'
 
     cloudProcess = false
 }
@@ -95,6 +96,19 @@ profiles {
         }
         includeConfig 'config/conda.config'
     }
+    docker {
+        docker { enabled = true }
+        includeConfig 'config/container.config'
+    }
+    singularity {
+        singularity { 
+                enabled = true
+                autoMounts = true
+                cacheDir = params.singularity_cache_dir
+                envWhitelist = "HTTPS_PROXY,HTTP_PROXY,http_proxy,https_proxy,FTP_PROXY,ftp_proxy"
+        }
+        includeConfig 'config/container.config'
+    }
 
     // no config for stub runs
     stub {

diff --git a/test/README.md b/test/README.md
@@ -11,15 +11,15 @@ With the following commands and data set, the mode subtype can be tested for Inf
 ### Running test set
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_h1n1.fasta'
 ```
 
 ### Running test set with metadata
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_h1n1.fasta' \
      --metadata 'test/metadata_h1n1.xlsx'
@@ -46,7 +46,7 @@ With the following commands and data set, the mode subtype can be tested for Inf
 ### Running test set
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_h3n2.fasta' \
      --subtype 'h3n2'
@@ -55,7 +55,7 @@ nextflow run main.nf \
 ### Running test set with metadata
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_h3n2.fasta' \
      --metadata 'test/metadata_h3n2.xlsx' \
@@ -83,7 +83,7 @@ With the following commands and data set, the mode subtype can be tested for Inf
 ### Running test set
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_vic.fasta' \
      --subtype 'vic'
@@ -92,7 +92,7 @@ nextflow run main.nf \
 ### Running test set with metadata
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_vic.fasta' \
      --metadata 'test/metadata_vic.xlsx' \
@@ -119,7 +119,7 @@ With the following commands and data set, the mode split can be tested for OpenF
 ### Running test set
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_combi.fasta' \
      --split 'OpenFlu'
@@ -128,7 +128,7 @@ nextflow run main.nf \
 ### Running test set with metadata
 
 ```bash
-nextflow run main.nf \
+nextflow run rki-mf1/VirusWarn-Flu -r <version> \
      -profile conda,local \
      --fasta 'test/openflu_combi.fasta' \
      --metadata 'test/metadata_combi.xlsx' \