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Develop for v0.27.0 #358
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Develop for v0.27.0 #358
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- If --quiet has been passed on the command line, suppress printing of any additional messages beyond those that come from Nextflow - Detect if params.quiet exists during channels input and in the INIT function - Fixes #283
- These are currently single-threaded
- Move biomart step outside of the compute_qc_stats function (avoid querying the server too frequently)
- Rename debarcode_10x_scatac_fastqs to barcode_10x_scatac_fastqs - Additional options fixed - Keep the barcodes in the fastq name for now
- Bwa mem uses the -C option to add barcodes from the fastq comments (now added by the barcode_10x_scatac_fastqs.sh script in singlecelltoolkit. - Index process now passes through the input bam as output - Simplify bwa main.nf with pipes
- Barcode, quality and corrected barcodes are now added into the fastq comments field
- Extracts and corrects barcode in one step
- cleanup br input tuple to trimming
- Includes scripts for processing BioRad data
- Remove option to use an alternate temp directory (instead use NXF_TEMP env variable, or map the /tmp volume in the container elsewhere)
- This may become a selectable option later on
- Load base config, and profile-specific settings separately
- Run MarkDuplicates, pipe the output to SortSam
- Use existing docker image - Use MarkDuplicatesSpark process
- Mapping now writes a bam to disk after fixmate - Marking duplicates is handled with Picard/GATK, also outputting a coordinate sorted and indexed bam - Derive readgroup from fastq prior to mapping; add this to the bam file with bwa (used in Picard/GATK)
- Docker image update - Fix params for saturation script
Implement check for config version
- When staging multiple cellranger fragments files, an input file collision would occur (files are named identically). This is fixed by adding a process to rename these files with the sample ID as a prefix.
…nglecelltoolkit container
…le_to_use_seurat_v3_falvor Fixes a bug not able to use seurat_v3 flavor Scanpy in hvg selection
Update Nextflow version from 20.10.0 to 21.04.3
- Input data is now in the proper format [sampleId, [bam, index], ... ]
Fix harmony_only workflow
- Take outs directory for Cell Ranger ARC, produce data channel with the '10x_arc_cellranger_mex_outs' label
- Documentation updates
This was referenced Dec 3, 2021
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Summary of changes
srapipeline not working for scATAC-seq data Closes [BUG] SRA workflow not working for scATAC-seq samples #348maxSizeoption (-Xoption ofprefetch) b5c7bae. This option should be set accordingly when runningsrapipeline.seurat,seurat_v3andcell_ranger