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Update pipeline overview #1031

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merged 7 commits into from
May 22, 2023
Merged

Update pipeline overview #1031

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afe882a
Update pipeline overview
adamrtalbot May 22, 2023
5e1d8f4
Revert nextflow.config
adamrtalbot May 22, 2023
088dead
Slight change to format
adamrtalbot May 22, 2023
ee4168c
CHANGELOG
adamrtalbot May 22, 2023
cfd9a74
CHANGELOG
adamrtalbot May 22, 2023
e428d43
Change wording of the pipeline summary...summary
adamrtalbot May 22, 2023
7779dc5
Remove VCF filtering tools
adamrtalbot May 22, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1014](https://github.com/nf-core/sarek/pull/1014) - `snpeff_db` is now only the `db` version and not `genome.db`
- [#1015](https://github.com/nf-core/sarek/pull/1015) - Increase default value for `--nucleotides_per_second` to `200000` resulting in 21 groups for `GATK.GRCh38`
- [#1019](https://github.com/nf-core/sarek/pull/1019) - Set a default registry outside of profile scope
- [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary

### Fixed

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31 changes: 22 additions & 9 deletions README.md
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Expand Up @@ -31,15 +31,28 @@ It's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/nf-

## Pipeline summary

By default, the pipeline currently performs the following:

- Sequencing quality control (`FastQC`)
- Map Reads to Reference (`BWA mem`)
- Mark Duplicates (`GATK MarkDuplicates`)
- Base (Quality Score) Recalibration (`GATK BaseRecalibrator`, `GATK ApplyBQSR`)
- Preprocessing quality control (`samtools stats`)
- Preprocessing quality control (`mosdepth`)
- Overall pipeline run summaries (`MultiQC`)
Depending on the options and samples provided, the pipeline can currently perform the following:

- Form consensus reads from UMI sequences (`fgbio`)
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this is not donw by default

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Do you want to include the required options here or shall we link to the usage docs section?

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Don't really have an opinion :D Just because at the top it says: run by default. I think the phrasing should fit together

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Ah I see. I'll update the top line.

- Sequencing quality control and trimming (`FastQC`, `fastp`)
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trimming is also not enalbed by default

- Map Reads to Reference (`BWA-mem` or `BWA-mem2` or `dragmap`)
- Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator`, `GATK ApplyBQSR`)
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CRAM files after MD

- Summarise alignment statistics (`samtools stats`, `mosdepth`)
- Variant calling (enabled by `--tools`, see [compatibility](https://github.com/nf-core/sarek/blob/master/docs/usage.md#which-variant-calling-tool-is-implemented-for-which-data-type)):
- `HaplotypeCaller`
- `freebayes`
- `mpileup`
- `Strelka2`
- `DeepVariant`
- `Mutect2`
- `Manta`
- `TIDDIT`
- `ASCAT`
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maybe also lower case similar to the other names

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I'll update so they all use the offical name format.

- `Control-FREEC`
- `CNVkit`
- `MSIsensor-pro`
- Variant filtering and annotation (`SnpEff`, `Ensembl VEP`)
- Summarise and represent QC (`MultiQC`)

<p align="center">
<img title="Sarek Workflow" src="docs/images/sarek_subway.png" width=60%>
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