Update pipeline overview #1031
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Update pipeline overview #1031
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maxulysse
reviewed
May 22, 2023
CHANGELOG.md
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| @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | |||
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| ### Changed | |||
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| - [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary | |||
maxulysse
approved these changes
May 22, 2023
| - Preprocessing quality control (`samtools stats`) | ||
| - Preprocessing quality control (`mosdepth`) | ||
| - Overall pipeline run summaries (`MultiQC`) | ||
| - 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.
| - Preprocessing quality control (`mosdepth`) | ||
| - Overall pipeline run summaries (`MultiQC`) | ||
| - Form consensus reads from UMI sequences (`fgbio`) | ||
| - Sequencing quality control and trimming (`FastQC`, `fastp`) |
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trimming is also not enalbed by default
| - Form consensus reads from UMI sequences (`fgbio`) | ||
| - Sequencing quality control and trimming (`FastQC`, `fastp`) | ||
| - 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
| - `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.
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Update pipeline description
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).