goodwright/flow-nf

Reusable modules used in Flow

flow-nf

This repository holds reusable modules, subworkflows and wrappers that underpin goodwright maintained pipelines. Full documentation on how to use this repo and contribute can be found here.

Links to documentation for specific modules and subworkflows can be found in the list below.

Modules

Subworkflows

Wrappers

• Demultiplex

flow-nf's Issues

Can demultiplex pipeline take multiple annotation sheets?

The demultiplex pipeline currently takes a single annotation sheet, which is fine for almost all cases. Flow lanes can have multiple annotation sheets, where there is a mix of, say, CLIP and RNA-Seq samples in a single multiplexed reads file. What would the options be for allowing multiple annotation sheets as inputs?

Having an arbitrary number might be hard, but we could hardcode say, 5 (--annotation, --annotation2 etc) of which only the first is required. The CLIP_SAMPLESHEET_TO_BARCODE module could then take multiple input CSVs and create a single barcode file (as the three columns that Ultraplex cares about would be in all annotation sheets).

Not super urgent, but will probably be required eventually.

Annotation sheet column names

In CLIP_SAMPLESHEET_TO_BARCODE, the following column names are sought:

five_prime = df_samplesheet["5prime_barcode"]
three_prime = df_samplesheet["3prime_barcode"]
sample_names = df_samplesheet["id"]

Unless it would break something else, could these be changed to '5' Barcode Sequence', '3' Barcode Sequence' and 'Sample Name' respectively?

Is CLIP_SAMPLESHEET_TO_BARCODE CLIP-specific?

The module which creates an Ultraplex barcode file from an annotation sheet is currently called CLIP_SAMPLESHEET_TO_BARCODE. There doesn’t seem to be anything specific to CLIP in this in terms of the columns it uses.

Unless there’s something CLIP specific I’ve missed, could it be renamed to simply SAMPLESHEET_TO_BARCODE (or ANNOTATION_SHEET_TO_BARCODE if we’re sticking to the convention that sample sheet = what preprocessing pipelines take to describe already demultiplexes samples and annotation sheet = description of multiplexed file).