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README.md

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# nf-scautoqc
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nf-scautoqc is the Nextflow implementation of scAutoQC pipeline used in Oliver et al, 2023.
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nf-scautoqc is the Nextflow implementation of [scAutoQC pipeline](https://teichlab.github.io/sctk/notebooks/automatic_qc.html) used in Oliver et al, 2024.
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## Contents:
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## Files:
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* `main.nf` - the Nextflow pipeline that executes scAutoQC pipeline.
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* `nextflow.config` - the configuration script that allows the processes to be submitted to IBM LSF on Sanger's HPC and ensures correct environment is set via singularity container (this is an absolute path). Global default parameters are also set in this file and some contain absolute paths.
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## Release notes
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### v0.2.2
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* Bug fixes
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### v0.2.1
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* Typo fix
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### v0.2.0
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* Improvements in python scripts
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* Changed output filenames in all scripts

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