Awesome
fastqc-nf
Quality control of raw sequencing reads
Description
Perform quality control of Fasta 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.
- FastQC: 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.)
- Multiqc: 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.)
BAM input files
In order to process BAM files, we convert fastq files to bam files with:
Input
| Name | Description |
|---|---|
| --input_folder | Folder containing FASTQ files |
| --output_folder | Path to output folder |
Parameters
Optional
| Name | Example value | Description |
|---|---|---|
| --ext | fastq.gz | Extension of files |
| --multiqc_config | none | config yaml file for multiqc |
| --cpu | 2 | Number of cpu used by fastqc |
| --mem | 10 | Size of memory used for mapping (in GB) |
Flags
Flags are special parameters without value.
| Name | Description |
|---|---|
| --help | Display help |
Usage
nextflow run IARCbioinfo/fastqc-nf -r v1.1 -profile singularity --input_folder input --output_folder results
To run the pipeline with docker or conda instead of singularity, just replace "-profile singularity" with "-profile docker" or "-profile conda", respectively. To run with your own local installation of softwares, just remove "-profile singularity"
Output
| Type | Description |
|---|---|
| multiqc_fastqc_report.html | multiQC report for fastQC |
| multiqc_fastqc_report_data | data used for the multiQC report HTMLs |
Contributions
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | AlcalaN@fellows.iarc.fr | Developer to contact for support |
| Tiffany Delhomme | Developer |