haplotyping-KIV2-nf Pipeline

haplotyping-KIV2-nf is a workflow tool to run tasks across multiple compute infrastructures in a very portable manner.

Overview

haplotyping-KIV2-nf is designed for haplotyping using a series of Python scripts. The workflow involves multiple stages such as filtering BAM files, extracting haplotypes, and merging haplotype information. The pipeline extracts the polymorphic positions of aligned reads provided in bam-file format. It removes the soft- and hard-clips of the sequences and extracts the polymorphic positions (haplotype) per sample either per-sample or using user defined positions.

Quick Start

1. Install nextflow

To run the haplotyping workflow, execute the following command:

nextflow run AmstlerStephan/haplotyping-KIV2-nf -r main -c <custom.config> -profile <docker/conda> 

Replace <path_to_input_directory> and <path_to_output_directory> with the actual paths.

Scripts and Files

• The workflow utilizes several Python scripts:
  • extract_haplotypes.py: Used for haplotype extraction.
  • merge_haplotypes.py: Used for merging haplotype information.
  • filter_bam.py: Used for filtering BAM files.
• Additionally, a file named variant_calling_positions is used for haplotype extraction. Its location is determined by the use_variant_calling_positions parameter.

Input Channels

• Input data is read from specific directories (input/barcode*/align/consensus/). BAM files, BAM file indexes, and cluster statistics are organized into tuples based on barcode information.

Workflow Stages

1. Filter BAM Files

   • Filters BAM files using the filter_bam.py script based on specified criteria.

2. Extract Haplotypes

   • Uses the extract_haplotypes.py script to extract haplotypes from the filtered BAM files. Haplotypes are filtered based on the provided variant_calling_positions file.

3. Merge Haplotypes

   • Merges the extracted haplotypes using the merge_haplotypes.py script.

Configuration

• The workflow may have configurable parameters in the nextflow.config file. Check for customization options there.

Basic Parameters

• help: A boolean flag indicating whether to display help information. Default is false.

• version: A boolean flag indicating whether to display the workflow version. Default is false.

• debug: A boolean flag enabling or disabling debug mode. When set to true, additional debugging information may be provided during workflow execution. Default is false.

Input/Output Parameters

• input: The directory containing input data for the workflow. This parameter is required for the workflow to locate and process input files.

• ont_pl_dir: The directory associated with the consensus reads obtained from the https://github.com/genepi/umi-pipeline-nf analysis workflow. Default is null.

• output: The directory where the workflow will write its output. This parameter is required for storing the results of the haplotyping workflow.

• variant_calling_positions: A file specifying variant calling positions. If provided, the workflow uses this file during haplotype extraction.

• bam_pattern: The pattern used to match BAM files within the input directory. Default is "masked_consensus.bam".

• cluster_stats_pattern: The pattern used to match cluster statistics files within the input directory. Default is "split_cluster_stats.tsv".

• min_reads_per_cluster: Minimum number of reads per cluster to be considered during processing. Default is 10.

• max_reads_per_cluster: Maximum number of reads per cluster to be considered during processing. Default is 200.

• max_edit_distance: Maximum edit distance allowed during merging of haplotype clusters. Default is 2.

• use_variant_calling_positions: A boolean flag indicating whether to use variant calling positions. If true, the workflow considers the variant_calling_positions file.

• ranges_to_exclude: A comma-separated list of ranges to exclude during processing. Default is "2472,2506".

• min_qscore: The minimum quality score required during processing. Default is 45.

• output_format: The output format for haplotype results. Default is "fasta".

Other Parameters

• threads: The number of threads used during workflow execution. It is set to (Runtime.runtime.availableProcessors() - 1) by default.

Output

• The workflow generates output files, including filtered BAM files, extracted haplotypes, and merged haplotype information.

Credits

These scripts were originally written for use by GENEPI, by (@StephanAmstler).