Update: Thu Jun 1 10:49:41 EDT 2023

README.md

@@ -7,7 +7,7 @@ This analysis pipeline is designed to analyze single-cell ATAC-Seq data and comb
 * This software has been tested on the following Linux operating systems: 64-bit CentOS 7 and 8, and Ubuntu 18.04.6, 20.04 LTS, 21.04, and 21.10.
     * The software may run on additional Linux distrubitions and/or versions beyond these if they are able to run the dependencies and versions listed below, but these are not officially supported.
 * Internet connection
-* [Nextflow](https://github.com/nextflow-io/nextflow#quick-start) (>=21.04.0)
+* [Nextflow](https://github.com/nextflow-io/nextflow#quick-start) (21.04.0-22.10.3)
 * [Docker](https://docs.docker.com/engine/install/) (>=20.10.7) or [Singularity](https://sylabs.io/guides/3.6/user-guide/quick_start.html#quick-installation-steps) (>=3.6.4)
 
 > **NOTE:** If using Docker, your `USER` must be added to the [`docker` root user group](https://docs.docker.com/engine/install/linux-postinstall/) before executing the pipeline. On shared systems, such as HPC clusters, this may not be possible due to security risks and the pipeline should be executed using the Singularity profile (default) instead.

containers/omnition-archr/Dockerfile

@@ -2,51 +2,50 @@
 
 # Copyright 2020 Bio-Rad Laboratories, Inc.
 
-# Starting with image already containing conda
-FROM continuumio/miniconda3:4.7.12
+# Starting with image already containing mamba
+FROM mambaorg/micromamba:1.0-bullseye-slim
 
 # Building image using bash shell
 SHELL ["/bin/bash", "-c"]
 
-# Name of conda environment being created (must match env.yaml filename)
-ARG CONDA_ENV="omnition-archr"
+# Name of mamba environment being created (must match env.yaml filename)
+ARG MAMBA_ENV="omnition-archr"
 
 # Installing image dependencies
-RUN apt-get --allow-releaseinfo-change update && \
-    apt-get install -y procps=2:3.3.15-2 && \
-    apt-get clean -y
+USER root
+RUN apt-get --allow-releaseinfo-change update \
+    && apt-get install -y procps=2:3.3.17-5 gawk=1:5.1.0-1 \
+    && apt-get clean -y
 
-# Building the conda environment
-COPY $CONDA_ENV.yaml /opt/biorad/env/
-RUN conda env create -f /opt/biorad/env/$CONDA_ENV.yaml && \
-    conda clean -afy
+# Building the mamba environment
+COPY $MAMBA_ENV.yaml /opt/biorad/env/
+RUN micromamba create -f /opt/biorad/env/$MAMBA_ENV.yaml \
+    && micromamba clean -afy
 
 # Removing default acitvation commands and setting correct ones
-RUN rm root/.bashrc
-RUN echo "source /etc/container.bashrc" >> /etc/bash.bashrc && \
-    echo "set +u" > /etc/container.bashrc && \
-    echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/container.bashrc && \
-    echo "conda activate $CONDA_ENV" >> /etc/container.bashrc
-
-# Adding in an empty folder to the BSgenome package which is required but not always installed depending on the source
-RUN mkdir -p /opt/conda/envs/${CONDA_ENV}/lib/R/library/BSgenome/pkgtemplates/BSgenome_datapkg/inst/extdata
+RUN rm /root/.bashrc
+RUN echo "source /etc/container.bashrc" >> /etc/bash.bashrc \
+    && echo "set +u" > /etc/container.bashrc \
+    && echo 'eval "$(micromamba shell hook --shell=bash)"' >> /etc/container.bashrc \
+    && echo "micromamba activate $MAMBA_ENV" >> /etc/container.bashrc
 
 # Activating environment when using non-login, non-interactive shell
 ENV BASH_ENV /etc/container.bashrc
 ENV ENV /etc/container.bashrc
 
-# Install Archr prereqs
-RUN apt-get install -y libcairo2-dev && \
-    Rscript -e 'BiocManager::install("TFBSTools")' && \
-    Rscript -e 'devtools::install_github("immunogenomics/presto", ref = "e7c9c6b708584aa23e590c5722bb5d35442f183d", upgrade = "never" , repos = BiocManager::repositories())' && \
-    apt-get install -y libxt-dev &&\
-    apt-get clean -y
+# Adding empty folder required for the BSgenome package
+RUN mkdir -p /opt/conda/envs/${MAMBA_ENV}/lib/R/library/BSgenome/pkgtemplates/BSgenome_datapkg/inst/extdata
 
 # Install ArchR
-RUN Rscript -e 'devtools::install_github("GreenleafLab/ArchR", ref = "48dccf361bab6d9191a4d9b61e1317acfa71167c", upgrade = "never", repos = BiocManager::repositories())'
-# RUN Rscript -e 'ArchR::installExtraPackages()'
+RUN Rscript -e 'devtools::install_github("GreenleafLab/ArchR", ref = "v1.0.2", upgrade = "never", repos = BiocManager::repositories())'
+RUN apt-get update \
+    && apt-get install -y libcairo2-dev \
+    && Rscript -e 'install.packages("Cairo", repos = "http://cran.us.r-project.org")' \
+    && Rscript -e 'ArchR::installExtraPackages()'
+
+# Adding Bio-Rad bin to path
+ENV PATH /opt/biorad/bin/:$PATH
 
 # Setting default working directory
 # WARNING: This is not preserved by Singularity
 WORKDIR /opt/biorad/
-

containers/omnition-report/Dockerfile

@@ -2,31 +2,32 @@
 
 # Copyright 2020 Bio-Rad Laboratories, Inc.
 
-# Starting with image already containing conda
-FROM continuumio/miniconda3:4.7.12
+# Starting with image already containing mamba
+FROM mambaorg/micromamba:1.0-bullseye-slim
 
 # Building image using bash shell
 SHELL ["/bin/bash", "-c"]
 
-# Name of conda environment being created (must match env.yaml filename)
-ARG CONDA_ENV="omnition-report"
+# Name of mamba environment being created (must match env.yaml filename)
+ARG MAMBA_ENV="omnition-report"
 
 # Installing image dependencies
-RUN apt-get --allow-releaseinfo-change update && \
-	apt-get install -y procps=2:3.3.15-2 && \
-	apt-get clean -y
+USER root
+RUN apt-get --allow-releaseinfo-change update \
+    && apt-get install -y procps=2:3.3.17-5 gawk=1:5.1.0-1 \
+    && apt-get clean -y
 
-# Building the conda environment
-COPY $CONDA_ENV.yaml /opt/biorad/env/
-RUN conda env create -f /opt/biorad/env/$CONDA_ENV.yaml && \
-	conda clean -afy
+# Building the mamba environment
+COPY $MAMBA_ENV.yaml /opt/biorad/env/
+RUN micromamba create -f /opt/biorad/env/$MAMBA_ENV.yaml \
+    && micromamba clean -afy
 
 # Removing default acitvation commands and setting correct ones
-RUN rm root/.bashrc
-RUN echo "source /etc/container.bashrc" >> /etc/bash.bashrc && \
-	echo "set +u" > /etc/container.bashrc && \
-	echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/container.bashrc && \
-	echo "conda activate $CONDA_ENV" >> /etc/container.bashrc
+RUN rm /root/.bashrc
+RUN echo "source /etc/container.bashrc" >> /etc/bash.bashrc \
+    && echo "set +u" > /etc/container.bashrc \
+    && echo 'eval "$(micromamba shell hook --shell=bash)"' >> /etc/container.bashrc \
+    && echo "micromamba activate $MAMBA_ENV" >> /etc/container.bashrc
 
 # Activating environment when using non-login, non-interactive shell
 ENV BASH_ENV /etc/container.bashrc
@@ -41,12 +42,12 @@ WORKDIR $APP_HOME
 RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
 
 # Install application
-RUN --mount=type=secret,id=GITHUB_TOKEN conda activate $CONDA_ENV && \
-    git clone --branch v1.0.3-alpha.1 \
-    https://$(cat /run/secrets/GITHUB_TOKEN):x-oauth-basic@github.com/BioRadOpenSource/cuttlesoft-single-cell-report.git ./ && \
-	for FILE in $(cat .dockerignore); do rm -rf $FILE; done && \
-    rm -rf .dockerignore .git* && \
-    npm i
+RUN --mount=type=secret,id=GITHUB_TOKEN micromamba activate $MAMBA_ENV \
+    && git clone --branch v1.0.3-alpha.1 \
+    https://$(cat /run/secrets/GITHUB_TOKEN):x-oauth-basic@github.com/BioRadOpenSource/cuttlesoft-single-cell-report.git ./ \
+    && for FILE in $(cat .dockerignore); do rm -rf $FILE; done \
+    && rm -rf .dockerignore .git* \
+    && npm i
 
 # Adding Bio-Rad bin to path
 ENV PATH /opt/biorad/bin/:$PATH

containers/omnition-report/omnition-report.yaml

@@ -1,11 +1,134 @@
 name: omnition-report
 channels:
-  - conda-forge
-  - bioconda
+- https://conda.anaconda.org/conda-forge
 dependencies:
-  - curl=7.83.1
-  - deepmerge=1.0.1
-  - matplotlib=3.5.1
-  - nodejs=12.19.0 
-  - pyreadr=0.4.4
-  - structlog=21.5.0
+- _libgcc_mutex=0.1=conda_forge
+- _openmp_mutex=4.5=2_gnu
+- alsa-lib=1.2.3.2=h166bdaf_0
+- attr=2.5.1=h166bdaf_1
+- brotli=1.0.9=h166bdaf_8
+- brotli-bin=1.0.9=h166bdaf_8
+- bzip2=1.0.8=h7f98852_4
+- c-ares=1.18.1=h7f98852_0
+- ca-certificates=2022.12.7=ha878542_0
+- certifi=2022.12.7=pyhd8ed1ab_0
+- curl=7.83.1=h7bff187_0
+- cycler=0.11.0=pyhd8ed1ab_0
+- dbus=1.13.6=h5008d03_3
+- deepmerge=1.0.1=pyhd8ed1ab_0
+- expat=2.5.0=h27087fc_0
+- fftw=3.3.10=nompi_hf0379b8_106
+- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+- font-ttf-inconsolata=3.000=h77eed37_0
+- font-ttf-source-code-pro=2.038=h77eed37_0
+- font-ttf-ubuntu=0.83=hab24e00_0
+- fontconfig=2.14.2=h14ed4e7_0
+- fonts-conda-ecosystem=1=0
+- fonts-conda-forge=1=0
+- fonttools=4.38.0=py310h5764c6d_1
+- freetype=2.12.1=hca18f0e_1
+- gettext=0.21.1=h27087fc_0
+- git=2.39.0=pl5321ha3eba64_0
+- gst-plugins-base=1.18.5=hf529b03_3
+- gstreamer=1.18.5=h9f60fe5_3
+- icu=68.2=h9c3ff4c_0
+- jack=1.9.18=hfd4fe87_1001
+- jpeg=9e=h0b41bf4_3
+- keyutils=1.6.1=h166bdaf_0
+- kiwisolver=1.4.4=py310hbf28c38_1
+- krb5=1.19.3=h3790be6_0
+- lcms2=2.14=hfd0df8a_1
+- ld_impl_linux-64=2.40=h41732ed_0
+- lerc=4.0.0=h27087fc_0
+- libblas=3.9.0=16_linux64_openblas
+- libbrotlicommon=1.0.9=h166bdaf_8
+- libbrotlidec=1.0.9=h166bdaf_8
+- libbrotlienc=1.0.9=h166bdaf_8
+- libcap=2.64=ha37c62d_0
+- libcblas=3.9.0=16_linux64_openblas
+- libclang=13.0.1=default_hc23dcda_0
+- libcups=2.3.3=h3e49a29_2
+- libcurl=7.83.1=h7bff187_0
+- libdb=6.2.32=h9c3ff4c_0
+- libdeflate=1.17=h0b41bf4_0
+- libedit=3.1.20191231=he28a2e2_2
+- libev=4.33=h516909a_1
+- libevent=2.1.10=h9b69904_4
+- libffi=3.4.2=h7f98852_5
+- libflac=1.3.4=h27087fc_0
+- libgcc-ng=12.2.0=h65d4601_19
+- libgfortran-ng=12.2.0=h69a702a_19
+- libgfortran5=12.2.0=h337968e_19
+- libglib=2.74.1=h606061b_1
+- libgomp=12.2.0=h65d4601_19
+- libiconv=1.17=h166bdaf_0
+- liblapack=3.9.0=16_linux64_openblas
+- libllvm13=13.0.1=hf817b99_2
+- libnghttp2=1.51.0=hdcd2b5c_0
+- libnsl=2.0.0=h7f98852_0
+- libogg=1.3.4=h7f98852_1
+- libopenblas=0.3.21=pthreads_h78a6416_3
+- libopus=1.3.1=h7f98852_1
+- libpng=1.6.39=h753d276_0
+- libpq=14.5=h72a31a5_3
+- libsndfile=1.0.31=h9c3ff4c_1
+- libsqlite=3.40.0=h753d276_0
+- libssh2=1.10.0=haa6b8db_3
+- libstdcxx-ng=12.2.0=h46fd767_19
+- libtiff=4.5.0=h6adf6a1_2
+- libtool=2.4.7=h27087fc_0
+- libudev1=252=h166bdaf_0
+- libuuid=2.32.1=h7f98852_1000
+- libuv=1.41.1=h7f98852_0
+- libvorbis=1.3.7=h9c3ff4c_0
+- libwebp-base=1.2.4=h166bdaf_0
+- libxcb=1.13=h7f98852_1004
+- libxkbcommon=1.0.3=he3ba5ed_0
+- libxml2=2.9.12=h72842e0_0
+- libzlib=1.2.13=h166bdaf_4
+- matplotlib=3.5.1=py310hff52083_0
+- matplotlib-base=3.5.1=py310h23f4a51_0
+- munkres=1.1.4=pyh9f0ad1d_0
+- mysql-common=8.0.32=h14678bc_0
+- mysql-libs=8.0.32=h54cf53e_0
+- ncurses=6.3=h27087fc_1
+- nodejs=12.19.0=h8b53aa1_3
+- nspr=4.35=h27087fc_0
+- nss=3.88=he45b914_0
+- numpy=1.23.4=py310h53a5b5f_1
+- openjpeg=2.5.0=hfec8fc6_2
+- openssl=1.1.1t=h0b41bf4_0
+- packaging=23.0=pyhd8ed1ab_0
+- pandas=1.5.3=py310h9b08913_0
+- pcre2=10.40=hc3806b6_0
+- perl=5.32.1=2_h7f98852_perl5
+- pillow=9.4.0=py310h023d228_1
+- pip=23.0=pyhd8ed1ab_0
+- pthread-stubs=0.4=h36c2ea0_1001
+- pulseaudio=14.0=hbc9ff1d_7
+- pyparsing=3.0.9=pyhd8ed1ab_0
+- pyqt=5.15.4=py310hd8f1fbe_0
+- pyqt5-sip=12.9.0=py310hd8f1fbe_0
+- pyreadr=0.4.4=py310h957f721_1
+- python=3.10.8=h257c98d_0_cpython
+- python-dateutil=2.8.2=pyhd8ed1ab_0
+- python_abi=3.10=3_cp310
+- pytz=2022.7.1=pyhd8ed1ab_0
+- qt-main=5.15.2=hf8cb05d_0
+- readline=8.1.2=h0f457ee_0
+- setuptools=67.3.1=pyhd8ed1ab_0
+- sip=6.5.1=py310h122e73d_2
+- six=1.16.0=pyh6c4a22f_0
+- sqlite=3.40.0=h4ff8645_0
+- structlog=21.5.0=pyhd8ed1ab_0
+- tk=8.6.12=h27826a3_0
+- toml=0.10.2=pyhd8ed1ab_0
+- tornado=6.2=py310h5764c6d_1
+- tzdata=2022g=h191b570_0
+- unicodedata2=15.0.0=py310h5764c6d_0
+- wheel=0.38.4=pyhd8ed1ab_0
+- xorg-libxau=1.0.9=h7f98852_0
+- xorg-libxdmcp=1.1.3=h7f98852_0
+- xz=5.2.6=h166bdaf_0
+- zlib=1.2.13=h166bdaf_4
+- zstd=1.5.2=h3eb15da_6

nextflow.config

@@ -50,8 +50,8 @@ manifest {
     description = 'Bio-Rad Omnition analysis software for single-cell data.'
     defaultBranch = 'main'
     mainScript = 'main.nf'
-    nextflowVersion = '!>=21.04.0'
-    version = 'v1.0.0'
+    nextflowVersion = '!>=21.04.0, <=22.10.3'
+    version = 'v1.0.1'
     recurseSubmodules = true
 
 }
@@ -150,22 +150,23 @@ profiles {
 
 
 // Pipeline execution report settings
+def trace_timestamp = new java.util.Date().format( 'yyyyMMdd-HHmmss')
 report {
     enabled = true
-    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-execution_report.html" : "${params.outputDir}/pipeline_info/omnition-execution_report.html"
+    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-execution_report-${trace_timestamp}.html" : "${params.outputDir}/pipeline_info/omnition-execution_report-${trace_timestamp}.html"
 }
 timeline {
     enabled = true
-    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-timeline.html" : "${params.outputDir}/pipeline_info/omnition-timeline.html"
+    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-timeline-${trace_timestamp}.html" : "${params.outputDir}/pipeline_info/omnition-timeline-${trace_timestamp}.html"
 }
 trace {
     enabled = true
     fields = "task_id,hash,native_id,name,status,exit,submit,duration,realtime,cpus,%cpu,peak_rss,peak_vmem,rchar,wchar"
-    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-trace.txt" : "${params.outputDir}/pipeline_info/omnition-trace.txt"
+    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-trace-${trace_timestamp}.txt" : "${params.outputDir}/pipeline_info/omnition-trace-${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-dag.html" : "${params.outputDir}/pipeline_info/omnition-dag.html"
+    file = params.prefix ? "${params.outputDir}/pipeline_info/${params.prefix}-omnition-dag-${trace_timestamp}.html" : "${params.outputDir}/pipeline_info/omnition-dag-${trace_timestamp}.html"
 }