Skip to content

openpipeline 0.3.1

Choose a tag to compare

View all tags
@rcannood rcannood released this 08 Jun 13:51
· 1730 commits to main since this release
0.3.1
1190ed4

NEW FUNCTIONALITY

  • bin/port_from_czbiohub_utilities.sh: Added helper script to import components and pipelines from czbiohub/utilities

Imported components from czbiohub/utilities:

  • demux/cellranger_mkfastq: Demultiplex raw sequencing data.

  • mapping/cellranger_count: Align fastq files using Cell Ranger count.

  • mapping/cellranger_count_split: Split 10x Cell Ranger output directory into separate output fields.

Imported workflows from czbiohub/utilities:

  • workflows/1_ingestion/cellranger: Use Cell Ranger to preprocess 10x data.

  • workflows/1_ingestion/cellranger_demux: Use cellranger demux to demultiplex sequencing BCL output to FASTQ.

  • workflows/1_ingestion/cellranger_mapping: Use cellranger count to align 10x fastq files to a reference.

MINOR CHANGES

  • Fix interactive/run_cirrocumulus script raising NotImplementedError caused by using MutData.var_names_make_unique()
    on each modality instead of on the whole MuData object.

  • Fix transform/normalize_total and interactive/run_cirrocumulus component build missing a hdf5 dependency.

  • interactive/run_cellxgene: Updated container to ubuntu:focal because it contains python3.6 but cellxgene dropped python3.6 support.

  • mapping/bd_rhapsody_wta: Set --parallel to true by default.

  • mapping/bd_rhapsody_wta: Translate Bash script into Python.

  • download/sync_test_resources: Add --dryrun, --quiet, and --delete arguments.

  • convert/from_h5mu_to_seurat: Use eddelbuettel/r2u:22.04 docker container in order to speed up builds by downloading precompiled R packages.

  • mapping/cellranger_count: Use 5Gb for testing (to adhere to github CI runner memory constraints).

  • convert/from_bdrhap_to_h5ad: change test data to output from mapping/bd_rhapsody_wta after reducing the BD Rhapsody test data size.

  • Various config.vsh.yamls: Renamed values: to choices:.

  • download/download_file and transfer/publish: Switch base container from bash:5.1 to python:3.10.

  • mapping/bd_rhapsody_wta: Make sure procps is installed.

BUG FIXES

  • mapping/bd_rhapsody_wta: Use a smaller test dataset to reduce test time and make sure that the Github Action runners do not run out of disk space.

  • download/sync_test_resources: Disable the use of the Amazon EC2 instance metadata service to make script work on Github Actions runners.

  • convert/from_h5mu_to_seurat: Fix unit test requiring Seurat by using native R functions to test the Seurat object instead.

  • mapping/cellranger_count and bcl_demus/cellranger_mkfastq: cellranger uses the --parameter=value formatting instead of --parameter value to set command line arguments.

  • mapping/cellranger_count: --nosecondary is no longer always applied.

  • mapping/bd_rhapsody_wta: Added workaround for bug in Viash 0.5.12 where triple single quotes are incorrectly escaped (viash-io/viash#139).

DEPRECATED

  • bcl_demux/cellranger_mkfastq: Duplicate of demux/cellranger_mkfastq.
Assets 2
Loading