This repository has been archived by the owner on Apr 19, 2023. It is now read-only.
Develop_atac #362
Merged
Develop_atac #362
+3,923
−579
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- 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)
- collect() fragments and peaks files into a single channel to stage them in the working directory - Shorten the input tuple to only have the base filenames so that they are read from the current working directory
- New docker image - Updated process parameters, limit max polars threads to 6 - Enable sample-specific parameters
- Add qc documentation - Minor updates to preprocessing docs
- Fix detectino of gzip whitelists - Update docker container
- Updated polars and pyarrow packages - Fix for segfault in atac saturation script
- Remap bam/fragments output to be compatible with getDataChannel - Mix bam/fragments channels for input to qc steps
- In some tools there is little benefit to increasing the number of threads beyond a certain number. Limits are set now to 6 threads for adapter trimming and barcoding steps. This will allow more processes to run in parallel.
- Reformat headings, restructure sections - Update BioRad read details
- Check how many barcodes were corrected, throw error if the fraction falls below a threhold (~50%) - Update docker image - Add params for max_mismatches and min_frac_bcs_to_find to the barcode correction process
- Fix bug with gzip detection
- Two new keywords in the metatdata: hydrop_2x384 and hydrop_3x96. - Hydrop barcode extraction runs separately for each type, passing the parameter to the extract_hydrop_atac_barcode_from_R2_fastq.sh script - #352
- Resolves #352
- Docker image update - Fix params for saturation script
- 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.
- Input data is now in the proper format [sampleId, [bam, index], ... ]
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.