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Develop for 0.26.0 #341
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Develop for 0.26.0 #341
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- Revert to the Debian-based image after running into issues with memory errors in BWA
- Switch to local singularity container for development - Update publishing output - Add new configuration options for compute_qc_stats and cleanup the script - qc_filtering workflow update
- Skip samtools sort by name step
- Turn off compression for intermediate samtools steps
- Reduce the number of samtools threads to 6 or ${task.cpus}
- Major updates for Nextflow 20.10.0 compatibility
Use conda for building the environment Uses argparse instead of optparse
…inal h5ad output of the pipelines
- Separate functions to take in data from getDataChannel and get the bam and barcodes files for the cellranger-style data - For bam,tsv input, join these dataChannels together on sampleId - Automatically handle multiple input types from getDataChannel and these can be run simultaneously - Resolves #255
- Keep qc_filtering methods in a separate branch Revert "Update archr steps add option to remove density coloring on cell calling" - This reverts commit 69e46c3. Revert "Add additional output to cell calling step" - This reverts commit 77f3a4a. Revert "Refine pycistopic implementation andi compute_qc_stats function." - This reverts commit 0cff3a4. Revert "Add macs2 callpeaks command to qc_prefilter" - This reverts commit 162a1b3. Revert "Add archr qc filtering method and entry point" - This reverts commit 7606659. Revert "Update archr publish methods" - This reverts commit f9d54ba.
- Fixes incorrectly applied default settings when a process uses an additional label to specify compute resources (Fixes #323).
…_generic_inputs Feature/255 freemuxlet generic inputs
- When using tenx input for cellranger outs directories, an error would occur if there were multiple input paths separated by a comma. Now, the check for the number of paths returned is correct.
- Allow metadata to match to fewer than the full set of barcodes in the adata object (80% or more cells allowed)
…sources-labels Fix incorrectly applied compute resources settings
Updates to scATAC-seq preprocessing v1
dweemx
previously approved these changes
Jun 30, 2021
- when redirecting the home with `-H $PWD` the nextflow project
directory was no longer mounted in the container. Fixed by mounting
${HOME}/.nextflow/assets/
- Add a mount to direct /tmp into scratch space
- Add additional default options back into the profile
dweemx
approved these changes
Jun 30, 2021
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Summary of changes
adata object (80% or more cells allowed)
Updates to scATAC-seq preprocessing v1 (#334)
add_barcode_as_tagmawk script to include both corrected and uncorrected barcode tags in final bam