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Commit fcd35967 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
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changes in docs 0.5.0 carp

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docs/pipelines/carp.md
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......@@ -11,7 +11,7 @@ Carp is a pipeline for analyzing ChIP-seq NGS data. It uses the BWA MEM aligner
The layout of the sample configuration for Carp is basically the same as with our other multi sample pipelines, for example:
~~~
~~~ json
{
"samples": {
"sample_X": {
......@@ -58,19 +58,155 @@ While optional settings are:
As with other pipelines in the Biopet suite, Carp can be run by specifying the pipeline after the `pipeline` subcommand:
~~~
~~~ bash
java -jar </path/to/biopet.jar> pipeline carp -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
If you already have the `biopet` environment module loaded, you can also simply call `biopet`:
~~~
~~~ bash
biopet pipeline carp -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
It is also a good idea to specify retries (we recomend `-retry 4` up to `-retry 8`) so that cluster glitches do not interfere
It is also a good idea to specify retries (we recommend `-retry 4` up to `-retry 8`) so that cluster glitches do not interfere
with your pipeline runs.
## Example output
```bash
.
├── Carp.summary.json
├── report
│ ├── alignmentSummary.png
│ ├── alignmentSummary.tsv
│ ├── ext
│ │ ├── css
│ │ │ ├── bootstrap_dashboard.css
│ │ │ ├── bootstrap.min.css
│ │ │ ├── bootstrap-theme.min.css
│ │ │ └── sortable-theme-bootstrap.css
│ │ ├── fonts
│ │ │ ├── glyphicons-halflings-regular.ttf
│ │ │ ├── glyphicons-halflings-regular.woff
│ │ │ └── glyphicons-halflings-regular.woff2
│ │ └── js
│ │ ├── bootstrap.min.js
│ │ ├── jquery.min.js
│ │ └── sortable.min.js
│ ├── Files
│ │ └── index.html
│ ├── index.html
│ ├── insertsize.png
│ ├── insertsize.tsv
│ ├── QC_Bases_R1.png
│ ├── QC_Bases_R1.tsv
│ ├── QC_Bases_R2.png
│ ├── QC_Bases_R2.tsv
│ ├── QC_Reads_R1.png
│ ├── QC_Reads_R1.tsv
│ ├── QC_Reads_R2.png
│ ├── QC_Reads_R2.tsv
│ ├── Samples
│ │ ├── 10_Input_2
│ │ │ ├── Alignment
│ │ │ │ ├── index.html
│ │ │ │ ├── insertsize.png
│ │ │ │ ├── insertsize.tsv
│ │ │ │ ├── wgs.png
│ │ │ │ └── wgs.tsv
│ │ │ ├── Files
│ │ │ │ └── index.html
│ │ │ ├── index.html
│ │ │ └── Libraries
│ │ │ ├── 3307
│ │ │ │ ├── Alignment
│ │ │ │ │ ├── index.html
│ │ │ │ │ ├── insertsize.png
│ │ │ │ │ ├── insertsize.tsv
│ │ │ │ │ ├── wgs.png
│ │ │ │ │ └── wgs.tsv
│ │ │ │ ├── index.html
│ │ │ │ └── QC
│ │ │ │ ├── fastqc_R1_duplication_levels.png
│ │ │ │ ├── fastqc_R1_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_per_base_quality.png
│ │ │ │ ├── fastqc_R1_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_duplication_levels.png
│ │ │ │ ├── fastqc_R1_qc_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_qc_per_base_quality.png
│ │ │ │ ├── fastqc_R1_qc_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_sequence_length_distribution.png
│ │ │ │ ├── fastqc_R1_sequence_length_distribution.png
│ │ │ │ └── index.html
│ │ │ └── index.html
│ │ ├── 11_GR_2A
│ │ │ ├── Alignment
│ │ │ │ ├── index.html
│ │ │ │ ├── insertsize.png
│ │ │ │ ├── insertsize.tsv
│ │ │ │ ├── wgs.png
│ │ │ │ └── wgs.tsv
│ │ │ ├── alignmentSummary.png
│ │ │ ├── alignmentSummary.tsv
│ │ │ ├── Files
│ │ │ │ └── index.html
│ │ │ ├── index.html
│ │ │ └── Libraries
│ │ │ ├── 3307
│ │ │ │ ├── Alignment
│ │ │ │ │ ├── index.html
│ │ │ │ │ ├── insertsize.png
│ │ │ │ │ ├── insertsize.tsv
│ │ │ │ │ ├── wgs.png
│ │ │ │ │ └── wgs.tsv
│ │ │ │ ├── index.html
│ │ │ │ └── QC
│ │ │ │ ├── fastqc_R1_duplication_levels.png
│ │ │ │ ├── fastqc_R1_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_per_base_quality.png
│ │ │ │ ├── fastqc_R1_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_duplication_levels.png
│ │ │ │ ├── fastqc_R1_qc_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_qc_per_base_quality.png
│ │ │ │ ├── fastqc_R1_qc_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_sequence_length_distribution.png
│ │ │ │ ├── fastqc_R1_sequence_length_distribution.png
│ │ │ │ └── index.html
│ │ │ ├── 3385
│ │ │ │ ├── Alignment
│ │ │ │ │ ├── index.html
│ │ │ │ │ ├── insertsize.png
│ │ │ │ │ ├── insertsize.tsv
│ │ │ │ │ ├── wgs.png
│ │ │ │ │ └── wgs.tsv
│ │ │ │ ├── index.html
│ │ │ │ └── QC
│ │ │ │ ├── fastqc_R1_duplication_levels.png
│ │ │ │ ├── fastqc_R1_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_per_base_quality.png
│ │ │ │ ├── fastqc_R1_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_duplication_levels.png
│ │ │ │ ├── fastqc_R1_qc_kmer_profiles.png
│ │ │ │ ├── fastqc_R1_qc_per_base_quality.png
│ │ │ │ ├── fastqc_R1_qc_per_base_sequence_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_gc_content.png
│ │ │ │ ├── fastqc_R1_qc_per_sequence_quality.png
│ │ │ │ ├── fastqc_R1_qc_sequence_length_distribution.png
│ │ │ │ ├── fastqc_R1_sequence_length_distribution.png
│ │ │ │ └── index.html
│ │ │ └── index.html
```
## Getting Help
If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues).
......
docs/pipelines/flexiprep.md
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− 10
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# Flexiprep
## Introduction
Flexiprep is our quality control pipeline. This pipeline checks for possible barcode contamination, clips reads, trims reads and runs
the <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">Fastqc</a> tool.
Adapter clipping is performed by <a href="https://github.com/marcelm/cutadapt" target="_blank">Cutadapt</a>.
For quality trimming we use <a href="https://github.com/najoshi/sickle" target="_blank">Sickle</a>.
Flexiprep works on `.fastq` files.
Flexiprep is a quality control pipeline. This pipeline checks for possible barcode contamination, clips reads, trims reads and
runs [FASTQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter clipping is performed by [Cutadapt](https://github.com/marcelm/cutadapt).
For quality trimming we use [Sickle](https://github.com/najoshi/sickle).
Flexiprep only works on `.fastq` files.
## Example
To get the help menu:
~~~
``` bash
java -jar </path/to/biopet.jar> pipeline Flexiprep -h
Arguments for Flexiprep:
......@@ -21,17 +22,18 @@ Arguments for Flexiprep:
-library,--libid <libid> Library ID
-config,--config_file <config_file> JSON config file(s)
-DSC,--disablescatter Disable all scatters
~~~
```
Note that the pipeline also works on unpaired reads where one should only provide R1.
To start the pipeline (remove `-run` for a dry run):
~~~bash
``` bash
java -jar Biopet-0.2.0.jar pipeline Flexiprep -run -outDir myDir \
-R1 myFirstReadPair -R2 mySecondReadPair -sample mySampleName \
-library myLibname -config mySettings.json
~~~
```
## Configuration and flags
......@@ -64,7 +66,7 @@ The pipeline also outputs 2 Fastqc runs one before and one after quality control
### Example output
~~~
~~~ bash
.
├── mySample_01.qc.summary.json
├── mySample_01.qc.summary.json.out
......
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