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sanger-tol / ascc

A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.
https://pipelines.tol.sanger.ac.uk/ascc
MIT License
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README and docs/usage.md refer to FASTQC, not contamination screening of a genome assembly #45

Open talioto opened 3 months ago

talioto commented 3 months ago

Description of the bug

From the documentation, it is unclear how to run the pipeline. Why give a samplesheet with read files when the point is to decontaminate an assembly? These are the parameters: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' How is the assembly given? GRCh37 doesn't seem to be a path. Why give the reads? What are done with them. I don't need a FASTQC report. Please fix the documentation.

Command used and terminal output

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Relevant files

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System information

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DLBPointon commented 3 months ago

Hi Tyler, This pipeline is still in early development, so no none of the documentation matches the actual use case as of yet. This will change as the structure of the pipeline gets closer to completion. Currently, the CI/CD needs fixing, the data merging scripts need to be modularised and added along with busco BTK. Once these are complete we will have a complete pipeline structure which we can pre-release for public use.

The current yaml, for future reference, can be found in the most recent branch here: https://github.com/sanger-tol/ascc/blob/kmer_count/assets/github_testing/test.yaml

This will be added too and changed at short notice as we move from a 1 pipeline run 1 assembly system to a 1 run 3 + n assemblies (primary, haplo, cobiont) system.

Reads will be used to calculate the coverage information across the genomic assembly and provide graphs comparing GC% and coverage.

The final pipeline will be entirely configurable, so outside of the minimal pipeline, you will be able to pick and choose the sub-workflows you need in particular.