Release/1.1

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,42 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of LiuzLab/ai_marrvel _(eg. 1.1, 1.5, 1.8.2)_

.github/workflows/nf-core-lint.yml

@@ -0,0 +1,84 @@
+name: nf-core linting
+
+on:
+  push:
+    branches:
+      # - main
+      - "**"
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  pre-commit:
+    name: Run Pre-Commit Hooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          architecture: "x64"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
+
+  nf-core:
+    name: Run nf-core lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.10.1"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          architecture: "x64"
+
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+
+      - name: Upload linting log artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: nf-core-lint-logs
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt

.github/workflows/test.yml

@@ -20,7 +20,6 @@ jobs:
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           aws-region: ${{ secrets.AWS_REGION }}
 
-
       - name: Install jq
         run: sudo apt-get install jq
 
@@ -81,7 +80,6 @@ jobs:
           aws sqs delete-queue --queue-url ${{ steps.step_queue.outputs.queue_url }}
           echo "Queue deleted: ${{ steps.step_queue.outputs.queue_url }}"
 
-
       - name: Close Pull Request on Failure
         if: ${{ failure() }} && github.event_name == 'pull_request'
         run: |

.gitignore

@@ -1,23 +1,33 @@
 # General
 **/__pycache__
+**/.DS_Store
+.vscode/
 bcftools-1.9.tar.bz2
 run/bedtools
-.vscode/
-.DS_Store
-*/.DS_Store
 test_data/
 test_ref/
 test_output/
+**/.ipynb_checkpoints/
+*.ipynb
+.nfs*
 
 # Nextflow Related
-.nextflow*
-.nextflow/
-work/
-out/
-trace-*txt
-report-*html
-params.yaml
+/.nextflow*
+/.nextflow/
+/work*/
+/out*/
+/store*/
+/dag-*.html
+/trace-*.txt
+/report-*.html
+/timeline-*.html
+/params.yaml
 
 # Ignore R history and session files
 .Rhistory
 .RData
+
+# Ignore some files from model interpreter
+*/model_interpreter/results
+*/model_interpreter/templates
+*/model_interpreter/main.nf

.nf-core.yml

@@ -0,0 +1,43 @@
+repository_type: pipeline
+nf_core_version: 3.2.0
+
+lint:
+  pipeline_name_conventions: False # Ignore: Naming does not adhere to nf-core conventions: Contains uppercase letters
+  schema_lint: False # Ignore: Parameter input not found in schema
+  actions_awsfulltest: False
+  pipeline_todos: False
+  nextflow_config: False
+  multiqc_config: False
+  files_unchanged: False
+  files_exist:
+    - .gitattributes
+    - .editorconfig
+    - CHANGELOG.md
+    - CITATIONS.md
+    - CODE_OF_CONDUCT.md
+    - .github/.dockstore.yml
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - .github/workflows/ci.yml
+    - assets/multiqc_config.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/sendmail_template.txt
+    - assets/nf-core-AI_MARRVEL_logo_light.png
+    - conf/igenomes.config
+    - conf/igenomes_ignored.config
+    - conf/test.config
+    - conf/test_full.config
+    - docs/images/nf-core-AI_MARRVEL_logo_light.png
+    - docs/images/nf-core-AI_MARRVEL_logo_dark.png
+    - docs/output.md
+    - docs/README.md
+    - docs/usage.md
+    - ro-crate-metadata.json

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.0.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierignore

@@ -0,0 +1,12 @@
+email_template.html
+slackreport.json
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+bin/
+utils/

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: docs/source/requirements.txt
 
 sphinx:
-  configuration: docs/source/conf.py
+  configuration: docs/source/conf.py

Dockerfile

@@ -1,18 +1,7 @@
-# List of dependencies installed
-#	bcftools v1.9-1-deb_cv1
-#	ensemblorg/ensembl-vep:release_104.3
-#	python 2.7
-#	python 3.8.13
-#	R 4.2.1
-
-# dc7a542b7e1f
-#FROM ubuntu:18.04
-FROM ensemblorg/ensembl-vep:release_104.3
-USER root
-ENV DEBIAN_FRONTEND noninteractive
+FROM python:3.8
 
 # Install dependencies
-RUN apt-get update && apt-get install -y \
+RUN apt update && apt install -y \
     curl \
     git \
     build-essential \
@@ -22,54 +11,15 @@ RUN apt-get update && apt-get install -y \
     libbz2-dev \
     liblzma-dev \
     tabix \
-    python2.7 \
-    python3.8 \
-    python3.8-dev \
-    python3.8-distutils \
-    python3-apt
-
-RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
-RUN python3.8 get-pip.py
+    jq
 
 # Install python 3.8 dependencies
 COPY requirements.txt /opt/requirements.txt
 RUN pip3 install --upgrade pip
 RUN pip3 install -r /opt/requirements.txt
-RUN pip3 install bgzip
-
-
-# Install R
-RUN apt-get update
-RUN apt install -y --no-install-recommends software-properties-common dirmngr
-# Add the keys
-RUN apt install wget
-RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
-
-# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
-#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver ha.pool.sks-keyservers.net --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver pgp.mit.edu --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver keyserver.pgp.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-#RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-
-RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-RUN add-apt-repository universe
-RUN apt-get update
-
-RUN apt install -y r-base r-base-core  
-
-# Install R libs
-RUN R -e "install.packages('data.table',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('dplyr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('ontologyIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('ontologySimilarity',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('tidyverse',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-
-
 
 # Install bcftools
-RUN wget https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
+RUN curl -OL https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
 RUN mv bcftools-1.20.tar.bz2 /opt/bcftools-1.20.tar.bz2
 RUN tar -xf /opt/bcftools-1.20.tar.bz2 -C /opt/ && \
   rm /opt/bcftools-1.20.tar.bz2 && \
@@ -80,9 +30,6 @@ RUN tar -xf /opt/bcftools-1.20.tar.bz2 -C /opt/ && \
   rm -rf /opt/bcftools-1.20
 
 # Install bedtools
-RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
+RUN curl -OL https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
 RUN mv bedtools.static.binary /run/bedtools
 RUN chmod a+x /run/bedtools
-
-
-

Dockerfiles/oldpython.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.8
+
+RUN pip install scikit-learn==1.1.2
+RUN pip install pandas
+

Dockerfiles/r.Dockerfile

@@ -0,0 +1,5 @@
+FROM rocker/tidyverse
+
+# Install R libs
+RUN R -e "install.packages('ontologyIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('ontologySimilarity',dependencies=TRUE, repos='http://cran.rstudio.com/')"