Name | Description | Tools used |
---|---|---|
alignment-nf | Performs BAM realignment or fastq alignment, with/without local indel realignment and base quality score recalibration | bwa, samblaster, sambamba & in option: samtools, AdapterRemoval, GATK, k8 javascript execution shell, bwa-postalt.js |
BQSR-nf | Performs base quality score recalibration of bam files using GATK | samtools, samblaster, sambamba, GATK |
abra-nf | Runs ABRA (Assembly Based ReAligner) | ABRA, bedtools, bwa, sambamba, samtools |
RNAseq-nf | Performs RNAseq mapping, quality control, and reads counting - See also RNAseq_analysis_scripts for post-processing | fastqc, cutadapt, Python version > 2.7, trim_galore, RESeQC, multiQC, STAR, htseq & in option: hisat2, GATK, samtools |
GATK-Alignment-nf | Performs bwa alignment and pre-processing (realignment and recalibration) following GATK best practices (less performant than alignment-nf ) | bwa, picard, GATK |
Name | Description | Tools used |
---|---|---|
conpair-nf | Runs conpair (concordance and contamination estimator) | conpair, Python 2.7, numpy 1.7.0 or higher, scipy 0.14.0 or higher, GATK 2.3 or higher |
damage-estimator-nf | Runs "Damage Estimator" | Damage Estimator, samtools, R with GGPLOT2 package |
bamsurgeon-nf | Runs bamsurgeon with step of variant simulation | Python 2.7, bamsurgeon, R software (tested with R version 3.2.3) |
Name | Description | Tools used |
---|---|---|
platypus-nf | Runs Platypus (germline variant caller) | Platypus |
GATK-Calling-GVCF-nf | Runs variant calling in GVCF mode on bam files, joint genotyping and variant recalibration (SNPs and indels) following GATK best practices - still in development!! | GATK |
CODEX-nf | Performs copy number variant calling from whole exome sequencing data using CODEX | R with package Codex, Rscript |
needlestack | Performs multi-sample somatic variant calling | perl, bedtools, samtools and Rscript |
mutect-nf | Runs Mutect on tumor-matched normal bam pairs | Mutect and its dependencies (Java 1.7 and Maven 3.0+), bedtools |
strelka-nf | Runs Strelka | Strelka |
Name | Description | Tools used |
---|---|---|
addreplacerg-nf | Adds and replaces read group tags in BAM files | samtools |
-
Install java JRE if you don't already have it (7 or higher).
-
Install nextflow.
curl -fsSL get.nextflow.io | bash
And move it to a location in your
$PATH
(/usr/local/bin
for example here):sudo mv nextflow /usr/local/bin
You can update the nextflow sofware and the pipeline itself simply using:
nextflow -self-update
nextflow pull iarcbioinfo/pipeline_name
You can also automatically update the pipeline when you run it by adding the option -latest
in the nextflow run
command. Doing so you will always run the latest version from Github.
nextflow run iarcbioinfo/pipeline_name --help
Install docker.
This is very system specific (but quite easy in most cases), follow docker documentation. Also follow the optional configuration step called Create a Docker group
in their documentation.
To run nextflow pipeline with Docker, simply add the -with-docker
option.