iarcbioinfo/nf-hla-neo

iarcbioinfo/nf-hla-neo repository overview

⁠nf-hla-neo

Pipeline to predict neoantigens from WGS of T/N pairs

⁠Usage

#using a tn_pairs file
nextflow run iarcbioinfo/nf-hla-neo -r v1.0  \
-profile singularity --ref chr6.mhc.fa \
--tn_file cohort_neoantigen.tsv --cram_dir cram \
--vcf_dir vcfs --vep_dir vep-db-99 --output_folder results_hla_neo

⁠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.
External software:

You can avoid installing all the external software by only installing Docker or singularity. See the IARC-nf⁠ repository for more information.

⁠Input (mandatory)

Type	Description
--tn_file	[file] File containing list of T/N bam/cram files to be processed
--cram_dir	[dir] directory where the BAM or CRAM file are stored
--vcf_dir	[dir] directory where the VCF files are stored
--vep_dir	[dir] directory containing VEP database for annotation [hg38, GENCODE 33]
--ref	[file] fasta file of chr6 of reference genome [chr6-hg38.fa], shold be indexed with BWA-mem

⁠Example of cohort_neoantigen.tsv file (--tn_file)

A text file tabular separated, with the following header:

id      vcf     normal_cram     normal_id       tumor_id
sample1	sample1.vcf.gz	sample1_N.cram	NORMAL1	TUMOR1
sample2	sample2.vcf.gz	sample2_N.cram	sample2_N.cram	NORMAL2	TUMOR2
sample3	sample3.vcf.gz	sample3_N.cram	sample3_N.cram	NORMAL3	TUMOR3_1,TUMOR3_2

⁠Optional parameters

Name	type	Description
--pvactools_predictors	[string]	predictions tools to compute neoantigens [def:all_class_i,all_class_ii or NetMHCpan,NetMHCIIpan]
--bam	[flag]	active bam mode [def:cram]
--output_folder	[string]	name of output folder
--cpu	[Integer]	Number of CPUs[def:2]
--mem	[Integer]	Max memory [def:8Gb]

⁠Output

results
└── xHLA                        # HLA-typing predictions
│   ├── report-MESO_001-hla.json
│   ├── report-MESO_002-hla.json
│   ├── report-MESO_003-hla.json
│   ├── report-MESO_004-hla.json
│   ├── report-MESO_005-hla.json
│   ├── report-MESO_006-hla.json
│   ├── report-MESO_007-hla.json
│   ├── report-MESO_008-hla.json
│   ├── report-MESO_009-hla.json
├── VEP				# Annotation of variant impact
│   ├── MESO_001.vep.vcf
│   ├── MESO_002.vep.vcf
│   ├── MESO_003.vep.vcf
│   ├── MESO_004.vep.vcf
│   ├── MESO_005.vep.vcf
│   ├── MESO_006.vep.vcf
|
├── pVACTOOLS					#pvactools predictions
│   ├── MESO_002.pvactools.log			#pvactools log
│   ├── MESO_002_T1_pvactools				
│   │   ├── combined				 # neoatigens for class I and class II
│   │   │   ├── B00JALW.all_epitopes.aggregated.tsv    # raw predictions aggregated
│   │   │   ├── B00JALW.all_epitopes.tsv               # raw predictions 
│   │   │   └── B00JALW.filtered.tsv	               # filtered predictions
│   │   ├── MHC_Class_I				#neoatigens for class I
│   │   │   ├── B00JALW.all_epitopes.aggregated.tsv
│   │   │   ├── B00JALW.all_epitopes.tsv
│   │   │   ├── B00JALW.filtered.tsv
│   │   │   └── log
│   │   │       └── inputs.yml
│   │   └── MHC_Class_II			#neoatigens for class II
│   │       ├── B00JALW.all_epitopes.aggregated.tsv
│   │       ├── B00JALW.all_epitopes.tsv
│   │       ├── B00JALW.fasta
│   │       ├── B00JALW.filtered.tsv
│   │       └── log
|	         └── inputs.yml
├── nf-pipeline_info # Nextflow information directory
    ├── hla-neo_report.html
    ├── hla-neo_timeline.html
    ├── hla-neo_trace.txt
    └── run_parameters_report.txt # Custom file providing info for software versions and calling parameters

⁠Common errors

⁠vep-db

The first time is necesary to get a local copy of the vep database, you can achieve this by running the following command within the vep singularity container:

#get the singularity container
singularity pull docker://docker.io/iarcbioinfo/ensembl-vep:v1.0
#open a shell and run the folloing command
singularity shell ensembl-vep_v1.0.sif
#get a local copy of the vep cache database (gencode v33)
vep_install -a cf -s homo_sapiens -y GRCh38 -c vep-db-99 --CONVERT

⁠chr6 BWA index

To perform the HLA-typing this pipeline extract reads from the CRAM/BAM file and remap them to the chr6 of GRCh38 using BWA-MEM (0.7.15-r1140), hence the chr6.fa of GRCh38 should be indexed (BWA index) to perform the mapping of the reads.

⁠Singularity

The first time that the container is built from the docker image, the TMPDIR should be defined in a non parallel file-system, you can set this like:

export TMPDIR=/tmp

⁠Contributions

Name	Email	Description
Matthieu Foll*	[email protected]⁠	Developer to contact for support (link to specific gitter chatroom)
Alex Di Genova	[email protected]⁠	Developer

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