Awesome
Post alignement
Description
Perform a post alignement on aligned reads files.
Dependencies
- This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
- samtools: see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)
- sambamba : see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See theIARC-nf repository for more information.)
- bwakit : see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)
Input
| Name | Description |
|---|---|
| --input_folder | Folder containing Fasta files |
| --output_folder | Path to output folder |
Parameters
Optional
| Name | Example value | Description |
|---|---|---|
| samtools | /usr/bin/samtools | Path to samtools installation directory |
| sambamba | /usr/bin/sambamba | Path to sambamba installation directory |
| bwakit | /usr/bin/bwakit | Path to bwakit installation directory |
Flags
Flags are special parameters without value.
| Name | Description |
|---|---|
| --help | Display help |
Download test data set
git clone https://github.com/iarcbioinfo/data_test
Usage
nextflow run WGS_analysis/PostAlign.nf --samtools /path/to/samtools --sambamba /path/to/sambamba --bwait /path/to/bwakit --input_folder path/to/input --output_folder /path/to/output
Output
| Name | Description |
|---|---|
| Headers(*.HEAD) | First lines of the returned BAM file |
| BAMS(*.bam) | Improved alignment |