colData()
.k
s or resolutions.01_input_qc
stage also as a SCE object from a {drake}
cache.01_input_qc
stage."rds"
is now the default storage format for {drake}
cache.{drake}
-specific config parameters to config/pipeline.yaml
.DRAKE_MEMORY_STRATEGY
which can help on machines with low memory.arm64
architecture to download_yq()
.arm64
platform.scdrake_docker
vignette.scdrake
has been ported to a Docker image and this is now the recommended usage.vignette("scdrake_docker")
.scdrake
functions.vignette("scdrake_cli")
.run_single_sample()
and run_integration()
are now soft-deprecated.dev/run_check.R
and dev/run_tests.R
(former run_pipeline_tests.R
) now uses R-based CLI and are run through Rscript
.deps.Dockerfile
will install scdrake
with all dependencies from DESCRIPTION
.ADDITIONAL_CELL_DATA_FILE
parameter in 02_norm_clustering
stage
vignette.INTEGRATION_SOURCES
parameters has changed - please, review your configs.plan_custom.R
script in project directory.{SingleR}
was removed from DESCRIPTION
as the version for the current Bioconductor version
is available from the official Bioc repository. The GitHub version is compatible with Bioc 3.16 and caused
installation error on Bioc 3.15ENABLE_CELL_FILTERING
, ENABLE_GENE_FILTERING
).{clustermq}
version >= 0.8.8
, but show a warning if the version is greater.{SC3}
version if it is not installed from github.com/gorgitko/SC3
, but also allow version from Bioconductor.DRAKE_REBUILD
allowing to force rebuild targets.sce_final_norm_clustering
target where already present columns in colData()
were not updated by
new ones in the cell_data
target. This could happen when SCE object was imported in the 01_input_qc
stage
and already contained cluster assignments in colData()
from the previous scdrake
run.01_input_qc
stage report, added a line for emptyDroplets
lower bound in barcode rank plot.save_pdf()
is now able to treat invalid plots throwing an error on save.create_dummy_plot()
.02_norm_clustering
and 02_int_clustering
stage reports the PNG files are displayed and act as links to
associated multipage PDF files.NORM_CLUSTERING_DIMRED_PLOTS_OUT_DIR
and INT_CLUSTERING_DIMRED_PLOTS_OUT_DIR
,
respectively.{SingleR}
(https://github.com/LTLA/SingleR).renv.lock
.SingleCellExperiment
object saved as a Rds file.INPUT_DATA
parameter (replaces INPUT_10X_DIR
) in 01_input_qc.yaml
config.
Details can be found in vignette("stage_input_qc")
.EMPTY_DROPLETS_ENABLED
parameter).NORMALIZATION_TYPE: "none"
) as the input can be an already normalized
SingleCellExperiment
object (meaning it went through the {scdrake}
pipeline before).download_yq()
:download_yq()
now supports the masOS (darwin
)..exe
extension)..get_os()
.yq
tool's binary download on Windows..confirm_menu()
for non-interactive usage.init_project()
function.Add the following code to your website.
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