From 4b60e3664997e5912d62244832c25678a1ae7d1d Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <sajvanderzeeuw@sasc-sander.lumcnet.prod.intern>
Date: Mon, 1 Dec 2014 11:39:05 +0100
Subject: [PATCH] Changes in docs
---
docs/config.md | 49 +++++++++++++++++++++++++++++++-
docs/pipelines/basty.md | 11 +++++++
docs/pipelines/flexiprep.md | 2 +-
docs/tools/BastyGenerateFasta.md | 0
mkdocs.yml | 3 +-
5 files changed, 62 insertions(+), 3 deletions(-)
create mode 100644 docs/tools/BastyGenerateFasta.md
diff --git a/docs/config.md b/docs/config.md
index 1829cf0ea..c10419859 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -9,6 +9,7 @@ The sample config should be in [__JSON__](http://www.json.org/) format
- Third field contains __"R1" or "R2"__ or __"bam"__
- The fastq input files can be provided zipped and un zipped
+#### Example sample config
~~~
{
"samples":{
@@ -48,4 +49,50 @@ Note that there is a tool called [SamplesTsvToJson](tools/SamplesTsvToJson.md) t
### The settings config
-The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
\ No newline at end of file
+The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
+This config file should be written in JSON format. It can contain setup settings like references for the tools used,
+if the pipeline should use chunking or setting memory limits for certain programs almost everything can be adjusted trough this config file.
+One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
+E.g. in the example below the settings for Picard tools are altered only for Picard and not global.
+
+~~~
+"picard": { "validationstringency": "LENIENT" }
+~~~
+
+Global setting examples are:
+~~~
+"java_gc_timelimit": 98,
+"numberchunks": 25,
+"chunking": true
+~~~
+
+
+----
+
+#### Example settings config
+~~~
+{
+ "reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
+ "dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
+ "joint_variantcalling": false,
+ "haplotypecaller": { "scattercount": 100 },
+ "multisample": { "haplotypecaller": { "scattercount": 1000 } },
+ "picard": { "validationstringency": "LENIENT" },
+ "library_variantcalling_temp": true,
+ "target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
+ "min_dp": 5,
+ "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+ "bam_to_fastq": true,
+ "baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
+ "samtofastq": {"memory_limit": 8, "vmem": "16G"},
+ "java_gc_timelimit": 98,
+ "numberchunks": 25,
+ "chunking": true,
+ "haplotypecaller": { "scattercount": 1000 }
+}
+~~~
+
+### JSON validation
+
+To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
+website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
diff --git a/docs/pipelines/basty.md b/docs/pipelines/basty.md
index 076f2e2af..c415cba3f 100644
--- a/docs/pipelines/basty.md
+++ b/docs/pipelines/basty.md
@@ -1,5 +1,16 @@
# Introduction
+## [Basty](https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty)
+
+A pipeline for aligning bacterial genomes and detect structural variations on the level of SNPs. Basty will output phylogenetic trees.
+Which makes it very easy to look at the variations between certain species.
+
+# Tools
+* GATK-pipeline []()
+* FASTA builder [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
+* RAxml []()
+* Gubbins []()
+
# Invocation
# Example
diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index 8f8fc8d20..9ea2b2f37 100644
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
@@ -1,6 +1,6 @@
# Introduction
-# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/master/flexiprep)
+# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/develop/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep)
QC pipeline for fastq files
diff --git a/docs/tools/BastyGenerateFasta.md b/docs/tools/BastyGenerateFasta.md
new file mode 100644
index 000000000..e69de29bb
diff --git a/mkdocs.yml b/mkdocs.yml
index d0a13c333..3290092a9 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -2,13 +2,14 @@ site_name: Biopet user manual
pages:
- ['index.md', 'Home']
- ['config.md', 'Config']
-- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['pipelines/yamsvp.md', 'Pipelines', 'Yamsvp']
+- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
+- ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
- ['cluster/oge.md', 'OpenGridEngine']
- ['about.md', 'About']
- ['license.md', 'License']
--
GitLab