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add sentieon specific docs #175

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add sentieon specific docs
maxulysse Apr 2, 2020
4c33e25
reorder Custom resource requests section
maxulysse Apr 2, 2020
6f40568
add links to Sentieon docs
maxulysse Apr 2, 2020
666eb45
update CHANGELOG
maxulysse Apr 2, 2020
a154ab7
fix markdownlint
maxulysse Apr 2, 2020
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Apply suggestions from code review
maxulysse Apr 3, 2020
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Merge branch 'dev' into Sentieon
maxulysse Apr 3, 2020
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Merge branch 'dev' into Sentieon
maxulysse Apr 3, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -21,6 +21,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
- [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests
- [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation
- [#169](https://github.com/nf-core/sarek/pull/169) - Add `RELEASE_CHECKLIST.md` document
- [#169](https://github.com/nf-core/sarek/pull/169) - Add `Sentieon` documentation
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### Changed - [2.6dev]

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -69,6 +69,7 @@ The nf-core/sarek pipeline comes with documentation about the pipeline, found in
* [Documentation about containers](docs/containers.md)
4. [Output and how to interpret the results](docs/output.md)
* [Complementary information about ASCAT](docs/ascat.md)
* [Complementary information about Sentieon](docs/sentieon.md)
* [Extra documentation on annotation](docs/annotation.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)

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1 change: 1 addition & 0 deletions docs/README.md
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Expand Up @@ -15,5 +15,6 @@ The nf-core/sarek documentation is split into the following files:
* [Documentation about containers](containers.md)
4. [Output and how to interpret the results](output.md)
* [Complementary information about ASCAT](ascat.md)
* [Complementary information about Sentieon](sentieon.md)
* [Extra documentation on annotation](annotation.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
73 changes: 73 additions & 0 deletions docs/sentieon.md
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# nf-core/sarek: Usage with sentieon <!-- omit in toc -->

- [Introduction](#introduction)
- [Sentieon Analysis Pipelines & Tools](#sentieon-analysis-pipelines--tools)
- [Alignment](#alignment)
- [Germline SNV/INDEL Variant Calling - DNAseq](#germline-snvindel-variant-calling---dnaseq)
- [Germline SNV/INDEL Variant Calling - DNAscope](#germline-snvindel-variant-calling---dnascope)
- [Somatic SNV/INDEL Variant Calling - TNscope](#somatic-snvindel-variant-calling---tnscope)
- [Structural Variant Calling](#structural-variant-calling)
- [usage](#usage)
- [--sentieon](#--sentieon)
- [--tools](#--tools)

## Introduction

[Sentieon](https://www.sentieon.com/) is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency.

If [Sentieon](https://www.sentieon.com/) is available, use this `--sentieon` params to enable with Sarek to use some Sentieon Analysis Pipelines & Tools.

Please refer to the [nf-core/configs](https://github.com/nf-core/configs#adding-a-new-pipeline-specific-config) repository on how to make a pipeline-specific configuration file based on the [munin-sarek specific configuration file](https://github.com/nf-core/configs/blob/master/conf/pipeline/sarek/munin.config).

Or ask us on the [nf-core Slack](http://nf-co.re/join/slack) on the following channels: [#sarek](https://nfcore.slack.com/channels/sarek) or [#configs](https://nfcore.slack.com/channels/configs).

## Sentieon Analysis Pipelines & Tools

The following Sentieon Analysis Pipelines & Tools are available within Sarek.

### Alignment

> Sentieon BWA matches BWA-MEM with > 2X speedup.

This tool is enabled by default within Sarek if `--sention` is specified and if the pipeline is started with the `mapping` [step](usage.md#--step).
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### Germline SNV/INDEL Variant Calling - DNAseq

> Precision FDA award-winning software.
> Matches GATK 3.3-4.1, and without down-sampling.
> Results up to 10x faster and 100% consistent every time.

This tool is enabled within Sarek if `--sention` is specified and if `--tools DNAseq` is specified cf [--tools](#--tools).
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### Germline SNV/INDEL Variant Calling - DNAscope

> Improved accuracy and genome characterization.
> Machine learning enhanced filtering producing top variant calling accuracy.

This tool is enabled within Sarek if `--sention` is specified and if `--tools DNAscope` is specified cf [--tools](#--tools).
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### Somatic SNV/INDEL Variant Calling - TNscope

> Winner of ICGC-TCGA DREAM challenge.
> Improved accuracy, machine learning enhanced filtering.
> Supports molecular barcodes and unique molecular identifies.
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This tool is enabled within Sarek if `--sention` is specified and if `--tools TNscope` is specified cf [--tools](#--tools).
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### Structural Variant Calling

> Germline and somatic SV calling, including translocations, inversions, duplications and large INDELs

This tool is enabled within Sarek if `--sention` is specified and if `--tools DNAscope` is specified cf [--tools](#--tools).
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## usage

### --sentieon

Adds the following tools for the [`--tools`](#--tools) options: `DNAseq`, `DNAscope` and `TNscope`.

### --tools

For main usage of tools, follow the [usage/tools](usage.md#--tools) documentation.

With `--sentieon` the following tools options are also available within Sarek: `DNAseq`, `DNAscope` and `TNscope`.
66 changes: 32 additions & 34 deletions docs/usage.md
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Expand Up @@ -79,6 +79,11 @@
- [Job resources](#job-resources)
- [Automatic resubmission](#automatic-resubmission)
- [Custom resource requests](#custom-resource-requests)
- [--max_memory](#--max_memory)
- [--single_cpu_mem](#--single_cpu_mem)
- [--singleCPUMem](#--singlecpumem)
- [--max_time](#--max_time)
- [--max_cpus](#--max_cpus)
- [--markdup_java_options](#--markdup_java_options)
- [AWSBatch specific parameters](#awsbatch-specific-parameters)
- [--awsqueue](#--awsqueue)
Expand All @@ -97,11 +102,6 @@
- [-c](#-c)
- [--custom_config_version](#--custom_config_version)
- [--custom_config_base](#--custom_config_base)
- [--max_memory](#--max_memory)
- [--single_cpu_mem](#--single_cpu_mem)
- [--singleCPUMem](#--singlecpumem)
- [--max_time](#--max_time)
- [--max_cpus](#--max_cpus)
- [--plaintext_email](#--plaintext_email)
- [--monochrome_logs](#--monochrome_logs)
- [--multiqc_config](#--multiqc_config)
Expand Down Expand Up @@ -336,9 +336,7 @@ Available: `ASCAT`, `ControlFREEC`, `FreeBayes`, `HaplotypeCaller`, `Manta`, `mp
If [Sentieon](https://www.sentieon.com/) is available, use this to enable it for preprocessing, and variant calling.
Adds the following tools for the [`--tools`](#--tools) options: `DNAseq`, `DNAscope` and `TNscope`.

Please refer to the [nf-core/configs](https://github.com/nf-core/configs#adding-a-new-pipeline-specific-config) repository on how to make a pipeline-specific configuration file based on the [munin-sarek specific configuration file](https://github.com/nf-core/configs/blob/master/conf/pipeline/sarek/munin.config).

Or ask us on the [nf-core Slack](http://nf-co.re/join/slack) on the following channels: [#sarek](https://nfcore.slack.com/channels/sarek) [#configs](https://nfcore.slack.com/channels/configs).
More information in the [sention](sentieon.md) documentation.
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### --no_strelka_bp

Expand Down Expand Up @@ -778,7 +776,32 @@ You can then create a pull request to the `nf-core/configs` repository with the

If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).

## --markdup_java_options
### --max_memory

Use to set a top-limit for the default memory requirement for each process.
Should be a string in the format integer-unit eg. `--max_memory '8.GB'`

### --single_cpu_mem

Use to set memory for a single CPU.
Should be a string in the format integer-unit eg. `--single_cpu_mem '8.GB'`

### --singleCPUMem

> :warning: This params has been removed.
> Please check: [`--single_cpu_mem`](#--single_cpu_mem)

### --max_time

Use to set a top-limit for the default time requirement for each process.
Should be a string in the format integer-unit eg. `--max_time '2.h'`

### --max_cpus

Use to set a top-limit for the default CPU requirement for each process.
Should be a string in the format integer-unit eg. `--max_cpus 1`

### --markdup_java_options

To control the java options necessary for the GATK `MarkDuplicates` process, you can set this parameter. For example (those are the default settings):

Expand Down Expand Up @@ -902,31 +925,6 @@ nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs in one go for you, to make this process easier.

### --max_memory

Use to set a top-limit for the default memory requirement for each process.
Should be a string in the format integer-unit eg. `--max_memory '8.GB'`

### --single_cpu_mem

Use to set memory for a single CPU.
Should be a string in the format integer-unit eg. `--single_cpu_mem '8.GB'`

### --singleCPUMem

> :warning: This params has been removed.
> Please check: [`--single_cpu_mem`](#--single_cpu_mem)

### --max_time

Use to set a top-limit for the default time requirement for each process.
Should be a string in the format integer-unit eg. `--max_time '2.h'`

### --max_cpus

Use to set a top-limit for the default CPU requirement for each process.
Should be a string in the format integer-unit eg. `--max_cpus 1`

### --plaintext_email

Set to receive plain-text e-mails instead of HTML formatted.
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