Functions

This page documents helper functions defined in the pipeline.

Contents

• is_target_file
• is_excluded
• add_run_IDs_and_basecall_models_to_meta
• add_number_of_reads_to_meta
• fastq_ingress
• xam_ingress
• parse_arguments
• get_valid_inputs
• create_metamap
• get_target_files_in_dir
• get_sample_sheet

is_target_file

Defined in lib/ingress.nf:15

def is_target_file(file, extensions)

Check if a file ends with one of the target extensions.

Parameters

is_excluded

Defined in lib/ingress.nf:27

def is_excluded(p, margs)

Check if a file path is flagged for exclusion.

Parameters

add_run_IDs_and_basecall_models_to_meta

Defined in lib/ingress.nf:54

def add_run_IDs_and_basecall_models_to_meta(ch, allow_multiple_basecall_models)

Take a channel of the shape [meta, reads, path-to-stats-dir | null] (or [meta, [reads, index], path-to-stats-dir | null] in the case of XAM) and extract the run IDs and basecall model, from the run_ids and basecaller files in the stats directory, into the metamap. If the path to the stats dir is null, add an empty list.

Parameters

add_number_of_reads_to_meta

Defined in lib/ingress.nf:111

def add_number_of_reads_to_meta(ch, input_type_format)

Take a channel of the shape [meta, reads, path-to-stats-dir | null] and do the following:

• For fastcat, extract the number of reads from the n_seqs file.
• For bamstats, extract the number of primary alignments and unmapped reads from the bamstats.flagstat.tsv file. Then, add add these metrics to the meta map. If the path to the stats dir is null, set the values to 0 when adding them. If not set to 'fastq', input is assumed to be 'bam'.

Parameters

fastq_ingress

Defined in lib/ingress.nf:179

def fastq_ingress(arguments)

Take a map of input arguments, find valid FASTQ inputs, and return a channel with elements of [metamap, seqs.fastq.gz | null, path-to-fastcat-stats | null]. The second item is null for sample sheet entries without a matching barcode directory. The last item is null if fastcat was not run (it is only run on directories containing more than one FASTQ file or when stats: true).

• "input": path to either: (i) input FASTQ file, (ii) top-level directory containing FASTQ files, (iii) directory containing sub-directories which contain FASTQ files
• "sample": string to name single sample
• "sample_sheet": path to CSV sample sheet
• "analyse_unclassified": boolean. Whether to ingress unclassified (failed to demux) reads
• "analyse_fail": boolean. Whether to ingress any sequence files contained in *_fail directories.
• "stats": boolean whether to write the fastcat stats
• "fastcat_extra_args": string with extra arguments to pass to fastcat
• "required_sample_types": list of zero or more required sample types expected to be present in the sample sheet
• "per_read_stats": boolean. If true, output a bgzipped TSV containing a summary of each read to fastcat_stats/per-read-stats.tsv.gz.
• "fastq_chunk": null or a number of reads to place into chunked FASTQ files
• "allow_multiple_basecall_models": emit data of samples that had more than one basecall model; if this is false, such samples will be emitted as [meta, null, null] The first element is a map with metadata, the second is the path to the .fastq.gz file with the (potentially concatenated) sequences and the third is the path to the directory with the fastcat statistics. The second element is null for sample sheet entries for which no corresponding barcode directory was found. The third element is null if fastcat was not run.

Parameters

xam_ingress

Defined in lib/ingress.nf:288

def xam_ingress(arguments)

Take a map of input arguments, find valid (u)BAM inputs, and return a channel with elements of [metamap, reads.bam | null, path-to-bamstats-results | null]. The second item is null for sample sheet entries without a matching barcode directory or samples containing only uBAM files when keep_unaligned is false. The last item is null if bamstats was not run (it is only run when stats: true).

• "input": path to either: (i) input (u)BAM file, (ii) top-level directory containing (u)BAM files, (iii) directory containing sub-directories which contain (u)BAM files
• "sample": string to name single sample
• "sample_sheet": path to CSV sample sheet
• "analyse_unclassified": boolean. Whether to ingress unclassified (failed to demux) reads
• "analyse_fail": boolean. Whether to ingress any sequence files contained in *_fail directories.
• "stats": boolean whether to run bamstats
• "keep_unaligned": boolean whether to include uBAM files
• "return_fastq": boolean whether to convert to FASTQ (this will always run fastcat)
• "fastcat_extra_args": string with extra arguments to pass to fastcat
• "required_sample_types": list of zero or more required sample types expected to be present in the sample sheet
• "per_read_stats": boolean. If true, output a bgzipped TSV containing a summary
• "fastq_chunk": null or a number of reads to place into chunked FASTQ files
• "allow_multiple_basecall_models": boolean. If true, emit data of samples that had more than one basecall model; if this is false, such samples will be emitted as [meta, null, null] The first element is a map with metadata, the second is the path to the .bam file with the (potentially merged) sequences and the third is the path to the directory with the bamstats statistics. The second element is null for sample sheet entries for which no corresponding barcode directory was found and for samples with only uBAM files when keep_unaligned: false. The third element is null if bamstats was not run.

Parameters

parse_arguments

Defined in lib/ingress.nf:852

def parse_arguments(func_name, arguments, extra_kwargs)

Parse input arguments for fastq_ingress or xam_ingress. for details) the argument-parsing to be tailored to a particular ingress function)

Parameters

get_valid_inputs

Defined in lib/ingress.nf:886

def get_valid_inputs(margs, extensions)

Find valid inputs based on the target extensions and return a branched channel with branches missing, files and dir, which are of the shape [metamap, input_path | null] (with input_path pointing to a target file or a directory containing target files, respectively). missing contains sample sheet entries for which no corresponding barcodes were found. Checks whether the input is a single target file, a top-level directory with target files, or a directory containing sub-directories (usually barcodes) with target files.

Parameters

create_metamap

Defined in lib/ingress.nf:1123

def create_metamap(arguments)

Create a map that contains at least these keys: [alias, barcode, type]. alias is required, barcode and type are filled with default values if missing. Additional entries are allowed.

Parameters

get_target_files_in_dir

Defined in lib/ingress.nf:1149

def get_target_files_in_dir(dir, extensions, margs, recursive)

Get all target files below this directory.

Parameters

get_sample_sheet

Defined in lib/ingress.nf:1165

def get_sample_sheet(sample_sheet, required_sample_types)

Check the sample sheet and return a channel with its rows if it is valid. in the sample sheet

Parameters

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:27:31 UTC.