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IARC bioinformatics nextflow pipelines

Nextflow pipelines list

Raw NGS data processing

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

QC

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)

Variant calling

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

Other

Name Description Tools used
addreplacerg-nf Adds and replaces read group tags in BAM files samtools

Nextflow

Installation :

  1. Install java JRE if you don't already have it (7 or higher).

  2. 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

Configuration file

Pipelines updates :

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.

Display help :

nextflow run iarcbioinfo/pipeline_name --help

Docker

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.