test v0.1.7

.github/workflows/antigen_presentation_prediction.yml

@@ -0,0 +1,69 @@
+name: alignment
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Free disk space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+      with:
+        tool-cache: false
+        android: true
+        dotnet: true
+        haskell: true
+        large-packages: true
+        docker-images: true
+        swap-storage: true
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: "latest"
+        activate-environment: test-env
+        python-version: "3.10"
+
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        # Remove tmp files
+        sudo rm -rf /tmp/*
+
+        # Install conda packages
+        conda env list
+        conda info
+        conda config --add channels defaults
+        conda config --add channels bioconda
+        conda config --add channels conda-forge
+        conda config --set channel_priority strict
+        conda install pandas
+        conda install nextflow==23.10.0
+        conda install pylint
+        conda install coveralls
+        conda install pytest
+        conda install pytest-cov
+                
+        # Install nexus
+        pip install . --verbose
+
+    - name: Run linter
+      shell: bash -l {0}
+      run: |
+        chmod +x lint.sh
+        bash lint.sh
+
+    - name: Run unit tests
+      shell: bash -l {0}
+      run: |
+        chmod +x scripts/unittests/unittest_antigen_presentation_prediction.sh
+        bash scripts/unittests/unittest_antigen_presentation_prediction.sh

docker/dysgu/v1.6.7/Dockerfile

@@ -0,0 +1,83 @@
+# Use Ubuntu 22.04 LTS as the base image
+FROM ubuntu:22.04
+
+# Set noninteractive installation to avoid getting stuck during build
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages for Miniconda installation
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    autoconf \
+    automake \
+    build-essential \
+    bzip2 \
+    ca-certificates \
+    cmake \
+    curl \
+    gcc-12 \
+    gfortran \
+    git \
+    libarchive-dev \
+    libncurses-dev \
+    libpng-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libssl-dev \
+    libbz2-dev \
+    lzma-dev \
+    liblzma-dev \
+    libssl-dev \
+    libpcre2-dev \
+    libcurl4-openssl-dev \
+    make \
+    ncurses-dev \
+    openssl \
+    tzdata  \
+    wget \
+    zlib1g \
+    zlib1g-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and Install Miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.7.1-0-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh
+
+# Add Miniconda to PATH
+ENV PATH=/opt/conda/bin:$PATH
+ENV PATH=/opt/conda/lib:$PATH
+
+# Test conda installation by updating conda
+RUN conda update conda
+
+# Install samtools
+RUN wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 && \
+    tar -xvjf samtools-1.18.tar.bz2 && \
+    cd samtools-1.18/ && \
+    mkdir bin && \
+    ./configure --prefix=$(pwd) && \
+    make && \
+    make install
+
+# Add samtools to PATH
+ENV PATH /samtools-1.18:$PATH
+
+# Install bcftools
+RUN wget https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2 && \
+    tar -xvjf bcftools-1.18.tar.bz2 && \
+    cd bcftools-1.18/ && \
+    mkdir bin && \
+    ./configure --prefix=$(pwd) && \
+    make && \
+    make install
+
+# Add bcftools to PATH
+ENV PATH /bcftools-1.18:$PATH
+
+# Install dysgu
+RUN conda install -c conda-forge libgcc=13 openssl
+RUN conda install -c bioconda dysgu==1.6.7
+
+# Clean up to reduce Docker image size
+RUN apt-get clean

docker/mhcflurry2/v2.1.4/Dockerfile

@@ -0,0 +1,69 @@
+# Use Ubuntu 22.04 LTS as the base image
+FROM ubuntu:22.04
+
+# Set noninteractive installation to avoid getting stuck during build
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages for Miniconda installation
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    autoconf \
+    automake \
+    build-essential \
+    bzip2 \
+    ca-certificates \
+    cmake \
+    curl \
+    gcc-12 \
+    gfortran \
+    git \
+    libarchive-dev \
+    libncurses-dev \
+    libpng-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libssl-dev \
+    libbz2-dev \
+    lzma-dev \
+    liblzma-dev \
+    libssl-dev \
+    libpcre2-dev \
+    libcurl4-openssl-dev \
+    make \
+    ncurses-dev \
+    openssl \
+    tzdata  \
+    wget \
+    zlib1g \
+    zlib1g-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and Install Miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.7.1-0-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh
+
+# Add Miniconda to PATH
+ENV PATH=/opt/conda/bin:$PATH
+ENV PATH=/opt/conda/lib:$PATH
+
+# Test conda installation by updating conda
+RUN conda update conda
+
+# Install mhcflurry
+RUN conda config --set solver classic
+RUN conda install conda-forge::six==1.16.0
+RUN conda install pandas==2.2.2
+RUN conda install conda-forge::tensorflow==2.17.0
+RUN conda install conda-forge::keras==3.5.0
+RUN conda install conda-forge::appdirs==1.4.4
+RUN conda install anaconda::scikit-learn==1.5.1
+RUN conda install anaconda::pyyaml==6.0.1
+RUN conda install conda-forge::tqdm==4.66.5
+RUN pip install mhcgnomes==1.8.6
+RUN pip install mhcflurry
+RUN mhcflurry-downloads fetch
+
+# Clean up to reduce Docker image size
+RUN apt-get clean

docker/nanomonsv/v0.7.2/Dockerfile

@@ -0,0 +1,59 @@
+# Use Ubuntu 22.04 LTS as the base image
+FROM ubuntu:22.04
+
+# Set noninteractive installation to avoid getting stuck during build
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages for Miniconda installation
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    autoconf \
+    automake \
+    build-essential \
+    bzip2 \
+    ca-certificates \
+    cmake \
+    curl \
+    gcc-12 \
+    gfortran \
+    git \
+    libarchive-dev \
+    libncurses-dev \
+    libpng-dev \
+    libpcre3 \
+    libpcre3-dev \
+    libssl-dev \
+    libbz2-dev \
+    lzma-dev \
+    liblzma-dev \
+    libssl-dev \
+    libpcre2-dev \
+    libcurl4-openssl-dev \
+    make \
+    ncurses-dev \
+    openssl \
+    tzdata  \
+    wget \
+    zlib1g \
+    zlib1g-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and Install Miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.7.1-0-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh
+
+# Add Miniconda to PATH
+ENV PATH=/opt/conda/bin:$PATH
+ENV PATH=/opt/conda/lib:$PATH
+
+# Test conda installation by updating conda
+RUN conda update conda
+
+# Install nanomonsv
+RUN conda install -c conda-forge libgcc=13 openssl
+RUN conda install -c bioconda nanomonsv==0.7.2
+
+# Clean up to reduce Docker image size
+RUN apt-get clean

pyproject.toml

@@ -5,7 +5,7 @@ requires = [
 
 [project]
 name = "nexus"
-version = "0.1.6"
+version = "0.1.7"
 description = "NEXflow's Ultimate Streamliner"
 requires-python = ">=3.10"
 readme = "README.md"

scripts/data/bam/align_hg38_long_read_dna_fastq_files.sh

@@ -1,8 +1,17 @@
 nexus run --nf-workflow long_read_alignment_minimap2.nf \
   -c /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/nextflow/nextflow_test_docker.config \
   -w /Users/leework/Documents/Research/projects/project_nexus/data/processed/work/long_read_alignment_minimap2/ \
-  --samples_tsv_file /Users/leework/Documents/Research/projects/project_nexus/nexus/scripts/data/bam/samples_long_read_dna_fastq_files.tsv \
+  --samples_tsv_file /Users/leework/Documents/Research/projects/project_nexus/nexus/scripts/data/bam/samples_long_read_dna_fastq_files_1.tsv \
   --reference_genome_fasta_file /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fasta/hg38_chr17_1-8M_chr18_1-9M_hpv16.fa.gz \
   --reference_genome_fasta_fai_file /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fasta/hg38_chr17_1-8M_chr18_1-9M_hpv16.fa.gz.fai \
   --params_minimap2 '"-ax map-hifi --cs --eqx -Y -L"' \
   --output_dir /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/bam/
+
+nexus run --nf-workflow long_read_alignment_minimap2.nf \
+  -c /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/nextflow/nextflow_test_docker.config \
+  -w /Users/leework/Documents/Research/projects/project_nexus/data/processed/work/long_read_alignment_minimap2/ \
+  --samples_tsv_file /Users/leework/Documents/Research/projects/project_nexus/nexus/scripts/data/bam/samples_long_read_dna_fastq_files_2.tsv \
+  --reference_genome_fasta_file /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fasta/hg38_chr17_1-8M_chr18_1-9M_hpv16.fa.gz \
+  --reference_genome_fasta_fai_file /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fasta/hg38_chr17_1-8M_chr18_1-9M_hpv16.fa.gz.fai \
+  --params_minimap2 '"-ax map-hifi --cs -Y -L"' \
+  --output_dir /Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/bam/

scripts/data/bam/samples_long_read_dna_fastq_files_2.tsv

@@ -0,0 +1,3 @@
+sample_id	fastq_file
+sample001normal2	/Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fastq/sample001normal_long_read_dna.fastq.gz
+sample001tumor2	/Users/leework/Documents/Research/projects/project_nexus/nexus/test/data/fastq/sample001tumor_long_read_dna.fastq.gz

scripts/data/csv/create_sample900_mhcflurry2_input_csv_file.py

@@ -0,0 +1,10 @@
+import pandas as pd
+
+if __name__ == '__main__':
+    data = {
+        'peptide': ['SIINFEKL',
+                    'SIINFEKL'],
+        'allele': ['H-2-Kb',
+                   'H-2-Db']
+    }
+    pd.DataFrame(data).to_csv('../../../test/data/csv/sample900_mhcflurry2_input.csv', index=False)

scripts/data/fastq/create_sample001_long_read_dna_fastq_files.py

@@ -65,6 +65,7 @@ def create_fastq_file(
     # Step 2. Normal
     sequence = fasta.fetch("NC_000017.11:c7687490-7668421", 0, fasta.lengths[0])
     sequence = list(str(sequence))
+    sequence = sequence[0:2000] + sequence[2099:]
     sequence = ''.join(sequence)
 
     create_fastq_file(

scripts/unittests/unittest_antigen_presentation_prediction.sh

@@ -0,0 +1,6 @@
+pytest \
+  -s \
+  --cov-report=term-missing \
+  --cov=nexuslib \
+  test/ \
+  -k "test_antigen_presentation_prediction_mhcflurry2"

src/nexuslib/pipelines/alignment/long_read_alignment_minimap2/README.md

@@ -61,7 +61,7 @@ optional arguments:
 `-c`
 * Nextflow `config` file can be downloaded [here](https://github.com/pirl-unc/nexus/tree/main/nextflow)
 
-`--sample_tsv_file`
+`--samples_tsv_file`
 * A TSV (tab-separated values) file with the following headers:
 
 | Header     | Description                   |

src/nexuslib/pipelines/alignment/long_read_rna_alignment_ultra/README.md

@@ -58,7 +58,8 @@ optional arguments:
 `-c`
 * Nextflow `config` file can be downloaded [here](https://github.com/pirl-unc/nexus/tree/main/nextflow)
 
-`--sample_tsv_file`
+`--samples_tsv_file`
+* A TSV (tab-separated values) file with the following headers:
 
 | Header     | Description                  |
 | ---------- |------------------------------|

src/nexuslib/pipelines/alignment/paired-end_read_dna_alignment_bwa-mem2/README.md

@@ -87,7 +87,8 @@ optional arguments:
 `-c`
 * Nextflow config file can be downloaded [here](https://github.com/pirl-unc/nexus/tree/main/nextflow)
 
-`--sample_tsv_file`
+`--samples_tsv_file`
+* A TSV (tab-separated values) file with the following headers:
 
 | Header       | Description                     |
 | ------------ |---------------------------------|

src/nexuslib/pipelines/alignment/paired-end_read_rna_alignment_star/README.md

@@ -52,7 +52,8 @@ optional arguments:
 `-c`
 * Nextflow config file can be downloaded [here](https://github.com/pirl-unc/nexus/tree/main/nextflow)
 
-`--sample_tsv_file`
+`--samples_tsv_file`
+* A TSV (tab-separated values) file with the following headers:
 
 | Header       | Description                     |
 | ------------ |---------------------------------|