nanopore container splits

[x] nanopore container splits into nanopolish and medaka
[x] fixed issues with nanopolish, added numpy (1.21.0) and tensorflow (1.14.0)
[x] medaka version updated to 1.7.2
[x] --medaka-model added to medaka workflow.
[x] README updated
[ ] needs container updated on gms-Dockerhub.

.gitignore

@@ -2,6 +2,9 @@
 nextflow
 results
 *.sif
-work
+work/
 .idea/
 .DS_Store
+nanopore_medaka/
+nanopore_nanopolish/
+illumina_test/

README.md

@@ -102,6 +102,9 @@ nextflow run main.nf -profile singularity \
     --outdir illumina_test
 ```
 ### Nanopore nanopolish pipeline
+
+PLEASE NOTE: check the 'nextflow.config' is updated with 'gms-artic-nanopolish:latest'
+
 ```
 nextflow run main.nf -profile singularity \
     --nanopolish --prefix "test_nanopore_nanopolish" \
@@ -111,10 +114,14 @@ nextflow run main.nf -profile singularity \
     --outdir nanopore_nanopolish
 ```
 #### Nanopore medaka pipeline
+
+PLEASE NOTE: check the 'nextflow.config' is updated with 'gms-artic-medaka:latest'. To use the 'medka' workflow, please provide the '--medaka-model'. [Read more here](https://github.com/nanoporetech/medaka/tree/master#models) how to get the model information.
+
 ```
 nextflow run main.nf -profile singularity \
     --medaka --prefix "test_nanopore_medaka" \
     --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
+    --medaka-model [email protected]:variant \
     --outdir nanopore_medaka
 ```
 
@@ -142,6 +149,7 @@ nextflow run main.nf -profile singularity,sge \
 nextflow run main.nf -profile singularity,sge \
     --medaka --prefix "test_nanopore_medaka" \
     --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
+    --medaka-model [email protected]:variant \
     --outdir nanopore_medaka
 ```
 2. *for Illumina analysis*

conf/base.config

@@ -17,8 +17,8 @@ params{
 
 
     // Repo to download your primer scheme from
-    //schemeRepoURL = 'https://github.com/genomic-medicine-sweden/gms-artic.git'
-    schemeRepoURL = 'https://github.com/jd2112/gms-artic.git'
+    schemeRepoURL = 'https://github.com/genomic-medicine-sweden/gms-artic.git'
+    //schemeRepoURL = 'https://github.com/jd2112/gms-artic.git'
 
     // Directory within schemeRepoURL that contains primer schemes
     schemeDir = 'gms-artic'

conf/nanopore.config

@@ -34,5 +34,9 @@ params {
 
     // Minimum coverage depth to call aa consequences of variant.
     csqDpThreshold = 20
+
+    // medaka model used by artic minion
+    // {pore}_{device}_{caller variant}_{caller version}
+    medakaModel = '[email protected]:variant'
 
 }

environments/medaka/Dockerfile

@@ -0,0 +1,18 @@
+FROM continuumio/miniconda3:latest AS condabuild
+LABEL authors="Matt Bull" \
+      description="Docker image containing all requirements for the ARTIC project's ncov2019 pipeline"
+
+COPY environments/extras.yml /extras.yml
+COPY environments/medaka/environment.yml /environment.yml
+RUN /opt/conda/bin/conda install mamba -c conda-forge && \
+/opt/conda/bin/conda update mamba -c conda-forge && \
+/opt/conda/bin/mamba env create -f /environment.yml
+
+FROM debian:buster-slim
+RUN apt-get update && \
+apt-get install -y git procps && \
+apt-get clean -y
+COPY --from=condabuild /opt/conda/envs/artic /opt/conda/envs/artic
+ENV PATH=/opt/conda/envs/artic/bin:$PATH
+ENV LC_ALL C.UTF-8
+ENV LANG C.UTF-8

environments/medaka/Singularity

@@ -0,0 +1,35 @@
+Bootstrap: docker
+From: condaforge/mambaforge:latest
+Stage: condabuild
+
+%files
+environments/nanopore/environment.yml /environment.yml
+environments/extras.yml /extras.yml
+
+%labels
+authors="Matt Bull"
+description="Docker image containing all requirements for the ARTIC project's ncov2019 pipeline"
+
+%post
+/opt/conda/bin/mamba env create -f /environment.yml #&& \
+/opt/conda/bin/mamba env update -f /extras.yml -n artic
+
+Bootstrap: docker
+From: debian:buster-slim
+Stage: final
+
+%post
+apt-get update && \
+apt-get install -y git procps && \
+apt-get clean -y
+
+%files from condabuild
+/opt/conda/envs/artic /opt/conda/envs/artic
+
+%environment
+export PATH=/opt/conda/envs/artic/bin:$PATH
+export LC_ALL=C.UTF-8
+export LANG=C.UTF-8
+
+%runscript
+exec "/opt/conda/envs/artic/bin/artic" "$@"

environments/medaka/environment.yml

@@ -0,0 +1,11 @@
+condaname: artic
+channels:
+    - epi2melabs
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies:
+    - aplanat=0.5.4
+    - fastcat=0.3.6
+    - np-artic=1.3.0
+    - pomoxis=0.3.6

environments/medaka/extras.yml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - biopython
+  - matplotlib
+  - pandas
+  - samtools
+  - libxcb

environments/nanopolish/Dockerfile

@@ -0,0 +1,18 @@
+FROM continuumio/miniconda3:latest AS condabuild
+LABEL authors="Matt Bull" \
+      description="Docker image containing all requirements for the ARTIC project's ncov2019 pipeline"
+
+COPY environments/extras.yml /extras.yml
+COPY environments/nanopolish/environment.yml /environment.yml
+RUN /opt/conda/bin/conda install mamba -c conda-forge && \
+/opt/conda/bin/conda update mamba -c conda-forge && \
+/opt/conda/bin/mamba env create -f /environment.yml
+
+FROM debian:buster-slim
+RUN apt-get update && \
+apt-get install -y git procps && \
+apt-get clean -y
+COPY --from=condabuild /opt/conda/envs/artic /opt/conda/envs/artic
+ENV PATH=/opt/conda/envs/artic/bin:$PATH
+ENV LC_ALL C.UTF-8
+ENV LANG C.UTF-8

environments/nanopolish/Singularity

@@ -0,0 +1,35 @@
+Bootstrap: docker
+From: condaforge/mambaforge:latest
+Stage: condabuild
+
+%files
+environments/nanopore/environment.yml /environment.yml
+environments/extras.yml /extras.yml
+
+%labels
+authors="Matt Bull"
+description="Docker image containing all requirements for the ARTIC project's ncov2019 pipeline"
+
+%post
+/opt/conda/bin/mamba env create -f /environment.yml #&& \
+/opt/conda/bin/mamba env update -f /extras.yml -n artic
+
+Bootstrap: docker
+From: debian:buster-slim
+Stage: final
+
+%post
+apt-get update && \
+apt-get install -y git procps && \
+apt-get clean -y
+
+%files from condabuild
+/opt/conda/envs/artic /opt/conda/envs/artic
+
+%environment
+export PATH=/opt/conda/envs/artic/bin:$PATH
+export LC_ALL=C.UTF-8
+export LANG=C.UTF-8
+
+%runscript
+exec "/opt/conda/envs/artic/bin/artic" "$@"

environments/nanopolish/environment.yml

@@ -0,0 +1,24 @@
+name: artic
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - artic=1.1.3
+  - pyyaml=5.3.1
+  - python>=3.6
+  - pip=19.3.1
+  - gofasta=0.0.4
+  - usher=0.2.0
+  - snakemake-minimal=5.13
+  - minimap2=2.17
+  - nextclade=2.11
+  - fastqc=0.11.9
+  - rich=12.6.0
+  - multiqc=1.11
+  - numpy=<1.21.0
+  - tensorflow=1.14.0
+  - pip:
+      - pandas >= 1.1
+      - scikit-learn >= 0.23.1
+  - muscle=3.8

environments/nanopolish/extras.yml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - biopython
+  - matplotlib
+  - pandas
+  - samtools
+  - libxcb

modules/artic.nf

@@ -81,10 +81,12 @@ process articMinIONMedaka {
     """
     artic minion --medaka \
     ${minionFinalConfig} \
+    --medaka-model ${params.medakaModel} \
     --threads ${task.cpus} \
-    --scheme-directory ${schemeRepo} \
+    --scheme-directory ${params.schemeDir}/${params.scheme} \
     --read-file ${fastq} \
-    ${params.scheme}/${params.schemeVersion} \
+    --scheme-version ${params.schemeVersion} \
+    nCoV-2019-primer \
     ${sampleName}
     """
 }

nextflow.config

@@ -66,10 +66,12 @@ profiles {
           container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
         }
         withName:articMinIONMedaka {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
+          container="docker://genomicmedicinesweden/gms-artic-medka:latest"
+          //container="docker://jd21/gms-artic-medaka:latest"          
         }
         withName:articMinIONNanopolish {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
+          container="docker://genomicmedicinesweden/gms-artic-nanopolish:latest"
+          //container="docker://jd21/gms-artic-nanopolish:latest"          
         }
         withName:articRemoveUnmappedReads {
           container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"