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Update scripts in singlecelltoolkit image to latest git version. #380
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Update scripts in singlecelltoolkit image to latest git version.
Update pycistopic container.
Disable fragments file renaming for now.
Use Otsu thresholding for determining the number of cells.
Make calculation of saturation optional.
Fix saving of OTSU png file.
…run. Do not retrieve biomart gene annotation if it was done in a previous run. Also reformat/reorganise the script.
Try to limit the number of threads used by BAP when running R scripts.
Write pickle files in compute_qc_stats.py per sample.
Improve pycisTopic QC report notebook:
- Use proper functions.
- Try to fix multiprocessing hang.
- Use more fair "sampling" from input when chunking data for
running KDE in parallel.
Updated all processes with taylored CPU/MEM usage parameters.
…rsion. Update SAMtools Docker images to newer Debian version and samtools version.
Update bwamaptools Docker image with newer SAMtools base image.
…nd new/updated programs. Update singlecelltookit Docker image with newer SAMtools base image and new/updated programs.
Sort BAM file by coordinates while mapping with BWA.
Update SAMtools Docker images to SAMtools version 1.16.1.
…ase image. Update popscle Docker image so it uses the latest SAMtools image as base image.
Update TrimGalore Docker image and use latest cutadapt which should be a bit faster than the older versions.
Update singlecelltoolkit Docker image to the latest singlecelltoolkit git commit and rebase the base image to the lastest SAMtools Docker image.
Remove trailing whitespaces.
Escape "$" for bash variable in merge_sam_files.nf.
Add Barcard related scripts and workflows.
Add preliminary ATAC_PREPROCESS_RAPID workflow. It still requires some cleanup.
Update singlecelltoolkit toolkit to 2022-11-16-064b064.
Remove MERGE_BARCODE_MULTIPLETS import as it is not used yet.
Support NextFlow 21.10.x and higher, which does not support includes in workflows itself.
Use "nextflow.enable.dsl=2" instead of "nextflow.preview.dsl=2".
Update CONTRIBUTORS.md.
Add BAM merging step with SAMtools after mapping with BWA.
Publish merged BAM files or only BAM file per sample after BWA mapping.
Add Barcard container to pregenerated config file and add BAM index as input to create_fragments_from_bam.
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Update scripts in singlecelltoolkit image to latest git version.