auto_process_ngs.bcl2fastq.protocols

Defines the PROTOCOLS dictionary, which specifies the available Fastq generation protocols which can be used in the Fastq generation pipeline.

Each protocol is defined as a name (the dictionary key) and a dictionary of parameters (the dictionary value).

The following parameters compulsory for each protocol:

  • description: free-text string describing the protocol

  • pipeline_variant: a string specifying which of the implemented sub-pipelines the protocol will use; must be one of: “standard”, “10x_cellranger”, “10x_cellranger-atc”, “10x_cellranger-arc”, “10x_spaceranger”

  • supported_indexes: a sequence (list or tuple) which specifies the types of sample sheet index that the protocol supports; must be one or more of: “ILLUMINA”, “10X”, “NONE”

The remaining parameters can be none or more of any of the possible lane subset attributes. Most commonly:

  • r1_length

  • r2_length

  • r3_length

  • i1_length

  • i2_length

  • minimum_trimmed_read_lengths

  • mask_short_adapter_reads

  • no_lane_splitting

  • create_fastq_for_index_read

  • trim_adapters