Run SigProfilerAssignment with the pipeline output of HDP

[FerriolCalvet]

We still need to agree whether this is necessary or not, but if we want to implement it, this would be the way to go.

• Set an output channel for HDP signatures
• Pass this output to a new call to SigProfilerAssignment and use this as a reference signatures
• Make sure you set a proper definition on where the output should be stored

@rochamorro1
these could be the steps to follow I am adding it just for reference in case we want to solve it and so that we do not forget

[FerriolCalvet]

Personally I would tend to think that it is better to first run the different extraction methods within the pipeline and then take the extracted signatures that are trustworthy and use them as a "reference set of signatures" for all the following analysis with those samples, this could mean providing them as input to deepCSA in future runs.

but I am happy to find a different solution

[FerriolCalvet]

decompose_fit
Decomposes a set of de novo extracted mutational signatures into a known set of signatures (reference COSMIC signatures or customized signature databases) and assigns these known signatures into a given sample/s.

Two input files are required. First, a file containing the input somatic mutations, in any of the formats specified in the Using the Tool - Input section. Also, a matrix containing the de novo extracted mutational signatures, commonly derived from SigProfilerExtractor.

An optional third input file is needed in case a custom reference signature database is used. By default, reference COSMIC signatures v3.3 are used for decomposing the set of de novo extracted signatures.

Note: A reference genome build should also be specified if a mutation calling file is used as input.

from SigProfilerAssignment import Analyzer as Analyze
Analyze.decompose_fit(samples="path/to/input/mutations/file", 
                      output="path/to/output/folder",
                      input_type="desired/input/mutation/file/format",
                      signatures="path/to/input/denovo/signatures/file",
                      [signature_database="path/to/optional/reference/signatures/database/file",]
                      genome_build="GRCh37")