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scwatts committed Mar 15, 2024
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -30,7 +30,7 @@ available in oncoanalyser. The targeted sequencing workflow has built-in support
custom panels with externally-generated normalisation data.

The key analysis results for each sample are summarised and presented in an ORANGE report (summary page excerpt shown
below from *[COLO829_wgts.orange_report.pdf](https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/oncoanalyser/other/example_report/COLO829_wgts.orange_report.pdf)*):
below from _[COLO829_wgts.orange_report.pdf](https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/oncoanalyser/other/example_report/COLO829_wgts.orange_report.pdf)_):

<p align='center'><img width='750' src='docs/images/COLO829_wgts.orange_report.summary_section.png'></p>

Expand Down Expand Up @@ -107,7 +107,7 @@ Each release that is given extended support is allocated a separate long-lived g

Versions nominated to have current long-term support:

* TBD
- TBD

### Release parity

Expand All @@ -116,7 +116,7 @@ equivalence of these two pieces of software. The functional/feature parity with
in the below table.

| oncoanalyser | hmftools |
| --- | --- |
| ------------------- | -------- |
| 0.1.0 through 0.2.7 | 5.33 |
| 0.3.0 through 0.3.1 | 5.34 |

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15 changes: 10 additions & 5 deletions docs/output.md
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Expand Up @@ -86,14 +86,14 @@ hmftools.
[bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) is a short-read mapping tool used to align reads to a large reference
sequences. In oncoanalyser, bwa-mem2 is used to align DNA reads to the human genome.

*No outputs are published directly from bwa-mem2, see [MarkDups](#markdups) for the fully processed alignment outputs*
_No outputs are published directly from bwa-mem2, see [MarkDups](#markdups) for the fully processed alignment outputs_

#### STAR

[STAR](https://github.com/alexdobin/STAR) is a specialised mapping to used to align RNA reads to a reference
transcriptome.

*No outputs are published directly from STAR, see [Picard MarkDuplicates](#picard-markduplicates) for the fully processed alignment outputs*
_No outputs are published directly from STAR, see [Picard MarkDuplicates](#picard-markduplicates) for the fully processed alignment outputs_

### Alignment post-processing

Expand All @@ -116,7 +116,7 @@ transcriptome.
routines such as duplicate marking and unmapping of problematic regions. It can also handle UMIs when configured to do
so.

*MarkDups is only run on DNA alignments*
_MarkDups is only run on DNA alignments_

### Picard MarkDuplicates

Expand All @@ -133,7 +133,7 @@ so.
[Picard MarkDuplicates](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard) used to
mark duplicate reads following alignment.

*Picard MarkDuplicates is only run on RNA alignments*
_Picard MarkDuplicates is only run on RNA alignments_

### SNV, MNV, INDEL calling

Expand All @@ -143,10 +143,12 @@ mark duplicate reads following alignment.
<summary>Output files</summary>

- `<group_id>/sage/append/`

- `<tumor_dna_id>.sage.append.vcf.gz`: Tumor DNA sample small variant VCF with RNA data appended.
- `<normal_dna_id>.sage.append.vcf.gz`: Normal DNA sample small variant VCF with RNA data appended..

- `<group_id>/sage/somatic/`

- `<normal_dna_id>.sage.bqr.png`: Normal DNA sample base quality recalibration metrics plot.
- `<normal_dna_id>.sage.bqr.tsv`: Normal DNA sample base quality recalibration metrics.
- `<tumor_dna_id>.sage.bqr.png`: Tumor DNA sample base quality recalibration metrics plot.
Expand Down Expand Up @@ -198,7 +200,7 @@ information with regards to transcript and coding effects.
[SvPrep](https://github.com/hartwigmedical/hmftools/tree/master/sv-prep) runs prior to SV calling to reducing runtime by
rapidly identifying reads that are likely to be involved in a SV event.

*No outputs are published directly from SvPrep, see [GRIPSS](#gripss) for the fully processed SV calling outputs*
_No outputs are published directly from SvPrep, see [GRIPSS](#gripss) for the fully processed SV calling outputs_

#### GRIDSS

Expand All @@ -220,6 +222,7 @@ breakend/breakpoint assemblies to call variants.
<summary>Output files</summary>

- `<group_id>/gripss/germline/`

- `<tumor_dna_id>.gripss.filtered.germline.vcf.gz`: Filtered GRIDSS germline structural variants.
- `<tumor_dna_id>.gripss.filtered.germline.vcf.gz.tbi`: Filtered GRIDSS germline structural variants index.
- `<tumor_dna_id>.gripss.germline.vcf.gz`: GRIDSS structural variants (GRIPSS filters set but not applied).
Expand Down Expand Up @@ -319,6 +322,7 @@ purity/ploidy and annotates both small and structural variant calls with copy-nu
<summary>Output files</summary>

- `<group_id>/linx/germline_annotations/`

- `linx.version`: LINX version file.
- `<tumor_dna_id>.linx.germline.breakend.tsv`: Normal DNA sample breakend data.
- `<tumor_dna_id>.linx.germline.clusters.tsv`: Normal DNA sample clustered events.
Expand All @@ -328,6 +332,7 @@ purity/ploidy and annotates both small and structural variant calls with copy-nu
- `<tumor_dna_id>.linx.germline.svs.tsv`: Normal DNA sample structural variants.

- `<group_id>/linx/somatic_annotations/`

- `linx.version`: LINX version file.
- `<tumor_dna_id>.linx.breakend.tsv`: Tumor DNA sample breakend data.
- `<tumor_dna_id>.linx.clusters.tsv`: Tumor DNA sample clustered events.
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35 changes: 18 additions & 17 deletions docs/usage.md
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Expand Up @@ -23,23 +23,24 @@ locally to optimise execution or modified to create user-defined driver gene pan

> [!WARNING]
> There are important requirements when using BAMs as input instead of FASTQs:
> - STAR must have been run with [specific
> parameters](https://github.com/hartwigmedical/hmftools/tree/master/isofox#a-note-on-alignment-and-multi-mapping),
> this is critical for WTS data, and
> - reads are expected to have been aligned to one of the Hartwig-distributed reference genomes (user-defined genomes may be used though are not recommended)
>
> - STAR must have been run with [specific
> parameters](https://github.com/hartwigmedical/hmftools/tree/master/isofox#a-note-on-alignment-and-multi-mapping),
> this is critical for WTS data, and
> - reads are expected to have been aligned to one of the Hartwig-distributed reference genomes (user-defined genomes may be used though are not recommended)
## Supported analyses

A variety of analyses are accessible in oncoanalyser and are implicitly run according to the data available in the
samplesheet. The supported analysis types for each workflow are listed below.

| Input sequence data | WGS/WTS workflow | Targeted sequencing workflow<sup>\*</sup> |
| --- | :-: | :-: |
| • Tumor/normal DNA<br />• Tumor RNA | :white_check_mark: | - |
| • Tumor only DNA<br />• Tumor RNA | :white_check_mark: | :white_check_mark: |
| • Tumor/normal DNA | :white_check_mark: | - |
| • Tumor only DNA | :white_check_mark: | :white_check_mark: |
| • Tumor only RNA | :white_check_mark: | - |
| Input sequence data | WGS/WTS workflow | Targeted sequencing workflow<sup>\*</sup> |
| ----------------------------------- | :----------------: | :---------------------------------------: |
| • Tumor/normal DNA<br />• Tumor RNA | :white_check_mark: | - |
| • Tumor only DNA<br />• Tumor RNA | :white_check_mark: | :white_check_mark: |
| • Tumor/normal DNA | :white_check_mark: | - |
| • Tumor only DNA | :white_check_mark: | :white_check_mark: |
| • Tumor only RNA | :white_check_mark: | - |

<sub><sup>\*</sup> Supported analyses relate to the TSO500 panel only</sub>

Expand Down Expand Up @@ -106,7 +107,7 @@ P2__wgts,P2,SB,tumor,dna,fastq,library_id:SB_library;lane:001,/path/to/P2.SB.tum
### Column descriptions

| Column | Description |
| --- | --- |
| ------------- | -------------------------------------------------------------------- |
| group_id | Group ID for a set of samples and inputs |
| subject_id | Subject/patient ID |
| sample_id | Sample ID |
Expand All @@ -117,9 +118,9 @@ P2__wgts,P2,SB,tumor,dna,fastq,library_id:SB_library;lane:001,/path/to/P2.SB.tum

The identifiers provided in the samplesheet are used to set output file paths:

* `group_id`: top-level output directory for analysis files e.g. `output/COLO829_example/`
* tumor `sample_id`: output prefix for most filenames e.g. `COLO829T.purple.sv.vcf.gz`
* normal `sample_id`: output prefix for some filenames e.g. `COLO829R.cobalt.ratio.pcf`
- `group_id`: top-level output directory for analysis files e.g. `output/COLO829_example/`
- tumor `sample_id`: output prefix for most filenames e.g. `COLO829T.purple.sv.vcf.gz`
- normal `sample_id`: output prefix for some filenames e.g. `COLO829R.cobalt.ratio.pcf`

## Running the pipeline

Expand Down Expand Up @@ -247,15 +248,15 @@ nextflow run nf-core/oncoanalyser \
```

> [!WARNING]
> Providing existing inputs will cause oncoanalyser to skip the corresponding process but *not any* of the upstream
> Providing existing inputs will cause oncoanalyser to skip the corresponding process but _not any_ of the upstream
> processes.
### Configuring reference data

All reference data can be configured as needed. These are defined in various locations:

| Reference data | Filepath | Note |
| --- | --- | --- |
| ----------------------- | ------------------------- | --------------------------------------- |
| hmftools resource files | `conf/hmf_data.config` | Paths relative to data bundle directory |
| panel resource files | `conf/panel_data.config` | Paths relative to data bundle directory |
| Genomes and indexes | `conf/hmf_genomes.config` | Absolute paths |
Expand Down

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