Merge pull request #49 from friendsofstrandseq/dev

2.2.1: fixes

.gitignore

@@ -214,3 +214,4 @@ workflow/data/arbigent/scTRIP_segmentation.bed
 .tests/data_CHR17/RPE-BM510/bam/*.bam.raw
 .tests/data_CHR17/RPE-BM510/bam/*.bam.sort
 .tests/external_data/chr17.fa.log
+LOGS_DEV/

.gitpod.Dockerfile

@@ -0,0 +1,38 @@
+FROM gitpod/workspace-full:2023-03-24-02-48-18
+
+ENV RETRIGGER=4
+
+ENV BUILDKIT_VERSION=0.11.6
+ENV BUILDKIT_FILENAME=buildkit-v${BUILDKIT_VERSION}.linux-amd64.tar.gz
+ENV DAZZLE_VERSION=0.1.17
+
+USER root
+
+# Install dazzle, buildkit and pre-commit
+RUN curl -sSL https://github.com/moby/buildkit/releases/download/v${BUILDKIT_VERSION}/${BUILDKIT_FILENAME} | tar -xvz -C /usr
+RUN curl -sSL https://github.com/gitpod-io/dazzle/releases/download/v${DAZZLE_VERSION}/dazzle_${DAZZLE_VERSION}_Linux_x86_64.tar.gz | tar -xvz -C /usr/local/bin
+RUN curl -sSL https://github.com/mvdan/sh/releases/download/v3.5.1/shfmt_v3.5.1_linux_amd64 -o /usr/bin/shfmt \
+    && chmod +x /usr/bin/shfmt
+RUN install-packages shellcheck \
+    && pip3 install pre-commit
+RUN curl -sSL https://github.com/mikefarah/yq/releases/download/v4.22.1/yq_linux_amd64 -o /usr/bin/yq && chmod +x /usr/bin/yq
+
+# Apptainer installation
+RUN apt-get update && \
+    apt-get install -y software-properties-common && \
+    add-apt-repository -y ppa:apptainer/ppa && \
+    apt-get update && \
+    apt-get install -y apptainer
+
+# Mambaforge installation
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh && \
+    sh Mambaforge-Linux-x86_64.sh -b -p /home/gitpod/mambaforge && \
+    /home/gitpod/mambaforge/bin/mamba create -n snakemake -c bioconda -c conda-forge snakemake && \
+    /home/gitpod/mambaforge/bin/mamba init && \
+    echo "source /home/gitpod/mambaforge/bin/activate" >> /home/gitpod/.bashrc && \
+    echo "conda activate snakemake" >> /home/gitpod/.bashrc
+
+# Clean up to reduce image size
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm Mambaforge-Linux-x86_64.sh

.gitpod.yml

@@ -1,4 +1,72 @@
-image: condaforge/mambaforge:latest
+image:
+  file: .gitpod.Dockerfile
+
+ports:
+  - port: 5000
+    onOpen: ignore
+
 tasks:
+  - name: install pre-commit git hooks
+    init: pre-commit install
+  - name: start up buildkitd
+    command: |
+      sudo /usr/bin/buildkitd --debug  --config ./buildkitd.toml --group gitpod
+  - name: start a local docker registry
+    command: |
+      mkdir -p /workspace/registry
+      docker run -p 5000:5000 --name registry --rm -v /workspace/registry:/var/lib/registry registry:2
+    openMode: split-right
+  - name: dazzle build and test
+    command: |
+      gp ports await 5000
+      REPO=localhost:5000/dazzle
+      echo "To build specific chunks and combine them 'time ./build-chunk.sh  -c chunk1 -c chunk2:variant1.2.3 -n combo'"
+      echo "To build all the chunks and combinations 'time ./build-all.sh'"
+      echo "To build a specific combination 'time ./build-combo.sh combo'"
+      echo "To list image chunks 'dazzle project image-name $REPO'"
+      echo "To list hashes for image chunks 'dazzle project hash $REPO'"
+      echo "To print the combined image maniest 'dazzle project manifest $REPO'"
+
+    openMode: tab-after
+
+    # MOSAICATCHER
+
+    # MOSAICATCHER
+
+  - name: Change cache location
+    command: |
+      mkdir -p ~/my_mamba_cache
+      export CONDA_PKGS_DIRS=~/my_mamba_cache
+
   - name: Create snakemake env
-    command: mamba create -n snakemake -c bioconda -c conda-forge snakemake=7.18.2 -y
+    command: mamba create -n snakemake -c bioconda -c conda-forge snakemake -y
+
+  # - name: Run mosaicatcher
+  #   command: |
+  #     snakemake --configfile .tests/config/simple_config.yaml \
+  #       --config ashleys_pipeline=True MultiQC=True \
+  #       --profile workflow/snakemake_profiles/local/conda/ \
+  #       --conda-frontend mamba \
+  #       --cores 8 --forceall
+
+  # - name: Generate Dockerfile
+  #   command: |
+  #     snakemake --configfile .tests/config/simple_config.yaml \
+  #       --config ashleys_pipeline=True MultiQC=True \
+  #       --profile workflow/snakemake_profiles/local/conda/ \
+  #       --conda-frontend mamba \
+  #       --cores 8 --containerize
+
+vscode:
+  extensions:
+    - ms-azuretools.vscode-docker
+    - timonwong.shellcheck
+
+github:
+  prebuilds:
+    master: true
+    branches: true
+    pullRequests: true
+    pullRequestsFromForks: true
+    addCheck: true
+    addComment: true

.gitpod.yml.bak

@@ -0,0 +1,4 @@
+image: condaforge/mambaforge:latest
+tasks:
+  - name: Create snakemake env
+    command: mamba create -n snakemake -c bioconda -c conda-forge snakemake=7.18.2 -y

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-yaml
+        #  - args:
+        #    - --branch
+        #    - master
+        #    id: no-commit-to-branch
+    repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+  - hooks:
+      - id: snakefmt
+    repo: https://github.com/snakemake/snakefmt
+    rev: 0.4.0
+  - hooks:
+      - id: commitizen
+        stages:
+          - commit-msg
+    repo: https://github.com/commitizen-tools/commitizen
+    rev: v2.17.12

config/config.yaml

@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.0
+version: 2.2.1
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.0
+ashleys_pipeline_version: 2.2.1
 
 # Email for notifications about the pipeline's status
 email: ""

config/config_metadata.yaml

@@ -23,7 +23,7 @@ MultiQC:
   type: bool
   required: False
   default: False
-multistep_normalisation_analysis:
+multistep_normalisation:
   desc: "Enable / Disable multistep normalisation"
   type: bool
   required: False
@@ -38,11 +38,6 @@ ashleys_threshold:
   type: bool
   required: False
   default: 0.5
-plate_orientation:
-  desc: "Plate orientation for GC analysis (landscape/portrait)"
-  type: string
-  required: False
-  default: landscape
 window:
   desc: "Mosaic bin window size"
   type: int
@@ -73,7 +68,7 @@ samples_to_process:
   type: list
   required: True
   default: "[]"
-normalized_counts:
+hgsvc_based_normalized_counts:
   desc: Normalize or not mosaic counts
   type: bool
   required: False
@@ -116,3 +111,9 @@ scNOVA:
   required: False
   default: False
   lint_check: False
+genecore_prefix:
+  desc: ""
+  type: str
+  required: False
+  default: "/g/korbel/shared/genecore"
+  lint_check: False