The pipeline is seperated in four chained nextflow processes:

1. A BAM realignement process, which desaligns and realigns BAM files.
2. An indel realignment process, which performs a local realignment around indels.
3. A recalibration process from realigned BAM files.
4. A GVCF build process from recalibrated BAM files.

1. Install Samtools.
2. Install bwa
3. Install Sambamba.
4. Install Samblaster
5. Download GATK tools.

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

Also copy or move in your path samtools, bwa and sambamba.

Example:

nextflow run iarcbioinfo/GVCF_pipeline-nf --bam_folder BAM_test/

if all other mandatory parameters are defined in your ~/.nextflow/config.

• --bam_folder: Folder containing BAM files to be called.
• --fasta_ref: Reference fasta file (with index) (excepted if in your config).
• --GenomeAnalysisTK: GenomeAnalysisTK.jar file.
• --gold_std_indels: Gold standard GATK for indels.
• --phase1_indels: Phase 1 GATK for indels.
• --dbsnp: dbSNP mutations file.

• --cpu: Number of cpu used by bwa mem and sambamba (default: 8).

• --mem: Size of memory used by sambamba and bwa mem (in GB) (default: 32).

• --RG: Samtools read group specification with "\t" between fields (Default: "ID:bam_file_name\tSM:bam_file_name").

         e.g. --RG "PL:ILLUMINA\tDS:custom_read_group".
  

• --out_folder : Output folder (default: results_GVCF_pipeline).

• --intervals_gvcf: Bed file provided to GATK HaplotypeCaller.

All the parameters you want to use can be defined globally in your ~/.nextflow/config file as the following example:

profiles {
	standard {
                params {
                   hg19_ref = '/appli57/reference/GATK_Bundle/ucsc.hg19.fasta'
                   dbsnp = '/appli57/reference/GATK_Bundle/dbsnp_138.hg19_noMT.vcf'
                   GenomeAnalysisTK = '/appli57/GenomeAnalysisTK/GATK-3.4-0/GenomeAnalysisTK.jar'
                   gold_std_indels = '/appli57/reference/GATK_Bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf'
                   phase1_indels = '/appli57/reference/GATK_Bundle/1000G_phase1.indels.hg19.sites.vcf'
                }
}