Commit 812a1440 authored by Pappas's avatar Pappas
Browse files

Requested fixes

parent ea9a0b84
......@@ -7,7 +7,7 @@ by default to align ChIP-seq data and call the peaks and allows you to run all y
### Sample input extensions
Please refer [to our mapping pipeline](../mapping.md#Sample-input-extensions) for information about how the input samples should be handled.
Please refer to our [config documentation page](../../general/config.md) for information about how the input samples should be handled.
## Configuration File
......@@ -203,9 +203,6 @@ $ biopet pipeline carp -config </path/to/config.yml> \
-qsub -jobParaEnv BWA -run
~~~
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
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......@@ -22,7 +22,7 @@ You can also provide a `.refFlat` file containing ribosomal sequence coordinates
## Sample input extensions
Please refer [to our mapping pipeline](../mapping.md) for information about how the input samples should be handled.
Please refer [to our mapping pipeline](multisamplemapping.md) for information about how the input samples should be handled.
## Configuration File
As with other biopet pipelines, Gentrap relies on a JSON configuration file to run its analyses. There are two important parts here, the configuration for the samples (to determine the sample layout of your experiment) and the configuration for the pipeline settings (to determine which analyses are run).
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......@@ -75,7 +75,7 @@ Optional settings
| mapping | merge_strategy | String | preprocessmarkduplicates | Determines how the individual bam files from each library are merged into one bam file per sample. Available options: `preprocessmarkduplicates` (add read group information, mark duplicates and then merge), `mergesam` (simple samtools merge), `preprocessmergesam` (add read group information and merge with samtools), `markduplicates` (mark duplicates first and then merge), `preprocesssambambamarkdup` (add read group information, mark duplicates with sambamba and then merge), `none` (do not merge the bam files) |
| mapping | duplicates_method | String | picard | Determines the method to use for marking duplicates. Available options: `picard`, `sambamba` or `none` to disable duplicate marking |
| mapping | skip_flexiprep | Boolean| false | Determines whether the input is analysed with [Flexiprep](../flexiprep.md). |
| mapping | mapping_to_gears | String | all | Determines whether the input is analysed with [Gears](../gears.md) or not. Available options: `all` (all reads), `unmapped` (extract only the unmapped reads and analyse with Gears) and `none` (skip this step) |
| mapping | mapping_to_gears | String | none | Determines whether the input is analysed with [Gears](../gears.md) or not. Available options: `all` (all reads), `unmapped` (extract only the unmapped reads and analyse with Gears) and `none` (skip this step) |
An example config.yml
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