From adfa5d34633431faeaa01851ce50dcbcb6b69d55 Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Wed, 8 May 2024 13:28:51 -0700 Subject: [PATCH 1/4] remove --backend option --- workflows/cellranger/cellranger_arc_count.wdl | 8 ++++---- workflows/cellranger/cellranger_arc_mkfastq.wdl | 8 ++++---- workflows/cellranger/cellranger_atac_aggr.wdl | 4 ++-- workflows/cellranger/cellranger_atac_count.wdl | 8 ++++---- workflows/cellranger/cellranger_atac_create_reference.wdl | 2 +- workflows/cellranger/cellranger_atac_mkfastq.wdl | 8 ++++---- workflows/cellranger/cellranger_vdj_create_reference.wdl | 6 +++--- 7 files changed, 22 insertions(+), 22 deletions(-) diff --git a/workflows/cellranger/cellranger_arc_count.wdl b/workflows/cellranger/cellranger_arc_count.wdl index 80f79d7a..92472fe8 100644 --- a/workflows/cellranger/cellranger_arc_count.wdl +++ b/workflows/cellranger/cellranger_arc_count.wdl @@ -139,16 +139,16 @@ task run_cellranger_arc_count { directory = re.sub('/+$', '', directory) # remove trailing slashes target = samples[i] + '_' + str(i) try: - call_args = ['strato', 'exists', '--backend', '~{backend}', directory + '/' + samples[i] + '/'] + call_args = ['strato', 'exists', directory + '/' + samples[i] + '/'] print(' '.join(call_args)) check_call(call_args, stdout=DEVNULL, stderr=STDOUT) - call_args = ['strato', 'sync', '--backend', '~{backend}', '-m', directory + '/' + samples[i], target] + call_args = ['strato', 'sync', '-m', directory + '/' + samples[i], target] print(' '.join(call_args)) check_call(call_args) except CalledProcessError: if not os.path.exists(target): os.mkdir(target) - call_args = ['strato', 'cp', '--backend', '~{backend}', '-m', directory + '/' + samples[i] + '_S*_L*_*_001.fastq.gz' , target] + call_args = ['strato', 'cp', '-m', directory + '/' + samples[i] + '_S*_L*_*_001.fastq.gz' , target] print(' '.join(call_args)) check_call(call_args) fout.write(os.path.abspath(target) + ',' + samples[i] + ',' + ('Gene Expression' if data_types[i] == 'rna' else 'Chromatin Accessibility') + '\n') @@ -168,7 +168,7 @@ task run_cellranger_arc_count { check_call(call_args) CODE - strato sync --backend ~{backend} -m results/outs "~{output_directory}"/~{link_id} + strato sync -m results/outs "~{output_directory}"/~{link_id} } output { diff --git a/workflows/cellranger/cellranger_arc_mkfastq.wdl b/workflows/cellranger/cellranger_arc_mkfastq.wdl index 8c630b34..4881c28d 100644 --- a/workflows/cellranger/cellranger_arc_mkfastq.wdl +++ b/workflows/cellranger/cellranger_arc_mkfastq.wdl @@ -101,7 +101,7 @@ task run_cellranger_arc_mkfastq { export TMPDIR=/tmp export BACKEND=~{backend} monitor_script.sh > monitoring.log & - strato cp --backend ~{backend} -r -m ~{input_bcl_directory} . + strato cp -r -m ~{input_bcl_directory} . python < monitoring.log & - strato cp --backend '~{backend}' -m -r ~{input_bcl_directory} . + strato cp -m -r ~{input_bcl_directory} . python < Date: Wed, 8 May 2024 20:38:14 +0000 Subject: [PATCH 2/4] update docker images to use Stratocumulus v0.2.3 --- docker/cellranger-arc/2.0.2/Dockerfile | 2 +- docker/cellranger-atac/2.1.0/Dockerfile | 2 +- docker/cellranger/7.2.0/Dockerfile | 4 ++-- docker/cellranger/8.0.0/Dockerfile | 4 ++-- docker/config/0.3/Dockerfile | 1 + docker/cumulus_feature_barcoding/0.11.3/Dockerfile | 2 +- docker/spaceranger/3.0.0/Dockerfile | 4 ++-- 7 files changed, 10 insertions(+), 9 deletions(-) diff --git a/docker/cellranger-arc/2.0.2/Dockerfile b/docker/cellranger-arc/2.0.2/Dockerfile index 99400796..c4566eaf 100644 --- a/docker/cellranger-arc/2.0.2/Dockerfile +++ b/docker/cellranger-arc/2.0.2/Dockerfile @@ -15,7 +15,7 @@ RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.7.11.zip" -o "a RUN pip3 install --upgrade pip && \ pip3 install pandas==1.4.3 && \ pip3 install packaging==21.3 && \ - pip3 install stratocumulus==0.1.7 + pip3 install stratocumulus==0.2.3 RUN mkdir /software ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software diff --git a/docker/cellranger-atac/2.1.0/Dockerfile b/docker/cellranger-atac/2.1.0/Dockerfile index b9ee3278..58fa3c90 100644 --- a/docker/cellranger-atac/2.1.0/Dockerfile +++ b/docker/cellranger-atac/2.1.0/Dockerfile @@ -17,7 +17,7 @@ RUN ln -s /usr/bin/python3 /usr/bin/python RUN python -m pip install --upgrade pip && \ python -m pip install pandas==1.4.3 && \ python -m pip install packaging==21.3 && \ - python -m pip install stratocumulus==0.1.7 + python -m pip install stratocumulus==0.2.3 RUN mkdir /software ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software diff --git a/docker/cellranger/7.2.0/Dockerfile b/docker/cellranger/7.2.0/Dockerfile index 874f324e..f646d0ef 100644 --- a/docker/cellranger/7.2.0/Dockerfile +++ b/docker/cellranger/7.2.0/Dockerfile @@ -3,7 +3,7 @@ FROM debian:bullseye-slim SHELL ["/bin/bash", "-c"] RUN apt-get update && \ - apt-get install --no-install-recommends -y alien unzip rsync build-essential dpkg-dev curl gnupg procps python3 python3-pip + apt-get install --no-install-recommends -y unzip rsync build-essential dpkg-dev curl gnupg procps python3 python3-pip RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \ curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \ @@ -19,7 +19,7 @@ RUN ln -s /usr/bin/python3 /usr/bin/python RUN python -m pip install --upgrade pip --no-cache-dir && \ python -m pip install pandas==2.1.1 --no-cache-dir && \ python -m pip install packaging==23.2 --no-cache-dir && \ - python -m pip install stratocumulus==0.2.1 --no-cache-dir + python -m pip install stratocumulus==0.2.3 --no-cache-dir RUN mkdir /software ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software diff --git a/docker/cellranger/8.0.0/Dockerfile b/docker/cellranger/8.0.0/Dockerfile index 39655f3a..b49b05bb 100644 --- a/docker/cellranger/8.0.0/Dockerfile +++ b/docker/cellranger/8.0.0/Dockerfile @@ -3,7 +3,7 @@ FROM debian:bookworm-slim SHELL ["/bin/bash", "-c"] RUN apt-get update && \ - apt-get install --no-install-recommends -y alien unzip rsync build-essential dpkg-dev curl gnupg procps python3 python3-pip python3-venv + apt-get install --no-install-recommends -y unzip rsync build-essential dpkg-dev curl gnupg procps python3 python3-pip python3-venv RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \ curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \ @@ -20,7 +20,7 @@ ENV PATH=/software/python/bin:$PATH RUN python -m pip install --upgrade pip --no-cache-dir && \ python -m pip install pandas==2.2.1 --no-cache-dir && \ python -m pip install packaging==24.0 --no-cache-dir && \ - python -m pip install stratocumulus==0.2.1 --no-cache-dir + python -m pip install stratocumulus==0.2.3 --no-cache-dir ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software ADD cellranger-8.0.0.tar.gz /software diff --git a/docker/config/0.3/Dockerfile b/docker/config/0.3/Dockerfile index b906c1d6..d69ccf80 100644 --- a/docker/config/0.3/Dockerfile +++ b/docker/config/0.3/Dockerfile @@ -17,3 +17,4 @@ RUN apt-get -qq update && \ RUN mkdir /software ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/yiming/docker/config/check_uri.py /software +RUN chmod a+rx /software/* diff --git a/docker/cumulus_feature_barcoding/0.11.3/Dockerfile b/docker/cumulus_feature_barcoding/0.11.3/Dockerfile index 689f7e4b..138e17c0 100644 --- a/docker/cumulus_feature_barcoding/0.11.3/Dockerfile +++ b/docker/cumulus_feature_barcoding/0.11.3/Dockerfile @@ -34,7 +34,7 @@ RUN python -m pip install --upgrade pip --no-cache-dir && \ python -m pip install numpy==1.26.1 --no-cache-dir && \ python -m pip install pandas==2.1.1 --no-cache-dir && \ python -m pip install matplotlib==3.8.0 --no-cache-dir && \ - python -m pip install stratocumulus==0.2.1 --no-cache-dir + python -m pip install stratocumulus==0.2.3 --no-cache-dir RUN tar -xzf /software/0.11.3.tar.gz -C /software && \ cd /software/cumulus_feature_barcoding-0.11.3 && make clean && make all && cd ../.. && \ diff --git a/docker/spaceranger/3.0.0/Dockerfile b/docker/spaceranger/3.0.0/Dockerfile index 95359b79..0fef73ce 100644 --- a/docker/spaceranger/3.0.0/Dockerfile +++ b/docker/spaceranger/3.0.0/Dockerfile @@ -2,7 +2,7 @@ FROM debian:bookworm-slim SHELL ["/bin/bash", "-c"] RUN apt-get update && \ - apt-get install --no-install-recommends -y alien unzip build-essential dpkg-dev curl gnupg procps python3 python3-pip python3-venv + apt-get install --no-install-recommends -y unzip build-essential dpkg-dev curl gnupg procps python3 python3-pip python3-venv RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \ curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \ @@ -19,7 +19,7 @@ ENV PATH=/software/python/bin:$PATH RUN python -m pip install --upgrade pip --no-cache-dir && \ python -m pip install pandas==2.2.1 --no-cache-dir && \ python -m pip install packaging==24.0 --no-cache-dir && \ - python -m pip install stratocumulus==0.2.1 --no-cache-dir + python -m pip install stratocumulus==0.2.3 --no-cache-dir ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software ADD spaceranger-3.0.0.tar.gz /software From 94f00a330cc2f96c4b195ccdb849c7cc3d060823 Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Wed, 8 May 2024 14:00:03 -0700 Subject: [PATCH 3/4] update docs --- docs/cellranger/build_refs.rst | 12 ++++++------ docs/cellranger/fixed_rna_profiling.rst | 2 ++ docs/cellranger/sc_sn_rnaseq.rst | 6 ++++++ docs/spaceranger.rst | 21 ++++++++++++++++----- 4 files changed, 30 insertions(+), 11 deletions(-) diff --git a/docs/cellranger/build_refs.rst b/docs/cellranger/build_refs.rst index 8a58df20..8f7fb480 100644 --- a/docs/cellranger/build_refs.rst +++ b/docs/cellranger/build_refs.rst @@ -94,9 +94,9 @@ We provide a wrapper of ``cellranger mkref`` to build sc/snRNA-seq references. P - Ensembl v94 - * - cellranger_version - - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1 - - "7.1.0" - - "7.1.0" + - cellranger version, could be: 8.0.0, 7.2.0 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1 + - "8.0.0" + - "8.0.0" * - docker_registry - Docker registry to use for cellranger_workflow. Options: @@ -320,9 +320,9 @@ We provide a wrapper of ``cellranger mkvdjref`` to build single-cell immune prof - Ensembl v94 - * - cellranger_version - - cellranger version, could be: 7.2.0, 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1 - - "7.2.0" - - "7.2.0" + - cellranger version, could be: 8.0.0, 7.2.0, 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1 + - "8.0.0" + - "8.0.0" * - docker_registry - Docker registry to use for cellranger_workflow. Options: diff --git a/docs/cellranger/fixed_rna_profiling.rst b/docs/cellranger/fixed_rna_profiling.rst index d50863a1..58401e38 100644 --- a/docs/cellranger/fixed_rna_profiling.rst +++ b/docs/cellranger/fixed_rna_profiling.rst @@ -15,6 +15,8 @@ Sample Sheet - Description * - **GRCh38-2020-A** - Human GRCh38 (GENCODE v32/Ensembl 98) + * - **mm10-2020-A** + - Mouse mm10 (GENCODE vM23/Ensembl 98) #. *DataType* column. diff --git a/docs/cellranger/sc_sn_rnaseq.rst b/docs/cellranger/sc_sn_rnaseq.rst index e195d582..bf5bd50b 100644 --- a/docs/cellranger/sc_sn_rnaseq.rst +++ b/docs/cellranger/sc_sn_rnaseq.rst @@ -13,6 +13,12 @@ Sample sheet * - Keyword - Description + * - **GRCh38-2024-A** + - Human GRCh38, comparable to cellranger reference 2024-A (GENCODE v44/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.* + * - **GRCm39-2024-A** + - Mouse GRCm39, comparable to cellranger reference 2024-A (GENCODE vM33/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.* + * - **GRCh38_and_GRCm39-2024-A** + - Human GRCh38 (v44/Ensembl 110) and mouse GRCm39 (GENCODE vM33/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.* * - **GRCh38-2020-A** - Human GRCh38 (GENCODE v32/Ensembl 98) * - **mm10-2020-A** diff --git a/docs/spaceranger.rst b/docs/spaceranger.rst index a5607b34..8dd10047 100644 --- a/docs/spaceranger.rst +++ b/docs/spaceranger.rst @@ -71,10 +71,11 @@ Alternatively, users can submit jobs through command line interface (CLI) using * - **Sample** - Contains sample names. Each 10x channel should have a unique sample name. * - **Reference** - - - | Provides the reference genome used by Space Ranger for each 10x channel. - | The elements in the *reference* column can be either Google bucket URLs to reference tarballs or keywords such as *GRCh38-2020-A*. - | A full list of available keywords is included in each of the following data type sections (e.g. sc/snRNA-seq) below. + - Provides the reference genome used by Space Ranger for each 10x channel. The elements in the *reference* column can be either keywords of pre-built references or Google bucket URLs to reference tarballs. Below are available keywords of pre-built references: + + - **GRCh38-2020-A**: Human GRCh38 (GENCODE v32/Ensembl 98) + + - **mm10-2020-A**: Mouse mm10 (GENCODE vM23/Ensembl 98) * - **Flowcell** - | Indicates the Google bucket URLs of uploaded BCL folders. @@ -88,7 +89,17 @@ Alternatively, users can submit jobs through command line interface (CLI) using * - **Index** - Sample index (e.g. SI-GA-A12). * - ProbeSet - - Probe set for FFPE samples. **Choosing** from ``human_probe_v1`` (10x human probe set, CytoAssist-incompatible), ``human_probe_v2`` (10x human probe set, CytoAssist-compatible) and ``mouse_probe_v1`` (10x mouse probe set). Alternatively, a CSV file describing the probe set can be directly used. Setting ProbeSet to ``""`` for a sample implies the sample is not FFPE. + - Probe set for FFPE samples. Can be either a keyword or a cloud URI to a custom probe set. Below are keywords of available probe sets: + + - **human_probe_v2**: 10x human probe set version 2, CytAssist-compatible + + - **mouse_probe_v2**: 10x mouse probe set version 2, CytAssist-compatible + + - **human_probe_v1**: 10x human probe set version 1, CytAssist-compatible + + - **mouse_probe_v1**: 10x mouse probe set version 1, CytAssist-compatible + + **Notice:** Set ProbeSet to ``""`` for a sample implies the sample is not FFPE. * - Image - Cloud bucket url for a brightfield tissue H&E image in .jpg or .tiff format. This column is mutually exclusive with DarkImage and ColorizedImage columns. * - DarkImage From b56635006f98501a20aba5599a35aebc08e667be Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Wed, 8 May 2024 14:05:20 -0700 Subject: [PATCH 4/4] update release notes --- docs/conf.py | 2 +- docs/release_notes/version_2_6.rst | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 17a048fa..c74f072e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -26,7 +26,7 @@ # The short X.Y version version = '2.6' # The full version, including alpha/beta/rc tags -release = '2.6.0' +release = '2.6.1' # -- General configuration --------------------------------------------------- diff --git a/docs/release_notes/version_2_6.rst b/docs/release_notes/version_2_6.rst index 0572cef2..91518781 100644 --- a/docs/release_notes/version_2_6.rst +++ b/docs/release_notes/version_2_6.rst @@ -1,3 +1,11 @@ +2.6.1 :small:`May 8, 2024` +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +* In Cellranger workflow: Add new genome references for single-cell/nucleus RNA-Seq: **GRCh38-2024-A** for human, **GRCm39-2024-A** for mouse, and **GRCh38_and_GRCm39-2024-A** for human and mouse. +* In Spaceranger workflow: Add a new probe set **mouse_probe_v2** for mouse. +* Some underlying workflow improvement. + + 2.6.0 :small:`April 22, 2024` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^