icgc-argo-workflows/xml_variant_ingestion

ICGC ARGO variant calling pipeline which digest xml to vcf variant format

Input data:

Mapping file: test/data/sample_new.tsv

XML file: test/data/example.xml

Reference files:

test/reference/

hg19.fa Not provided, download needed https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz

hg19.fa.fai

hg38.fa.gz Not provided, download needed https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

hg38.fa.fai

hg38.dict

hg19ToHg38.over.chain.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

Usage

1. Download hg19.fa and hg38.fa.gz to test/reference/
2. Retrive api_token
3. Workflow command

Minimal Test

nextflow run main.nf \
    -profile docker,test,rdpc_qa \
    --api_token NNNNNNN \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test in RDPC-QA

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml /PATH/TO/XML.FILE \
    --experiment_info_tsv /PATH/TO/MAPPING.TSV \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data (Original)

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/example.xml \
    --experiment_info_tsv ./test/data/sample_new.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test1 - ORD-0000001-01.xml - short-variants/copy-number-alterations )

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/ORD-0000001-01.xml \
    --experiment_info_tsv ./test/data/sample_1.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test2 - ORD-0000002-01.xml - short-variants )

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/ORD-0000002-01.xml \
    --experiment_info_tsv ./test/data/sample_2.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test3 - ORD-0000003-01.xml - short-variants )

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/ORD-0000003-01.xml \
    --experiment_info_tsv ./test/data/sample_3.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test4 - ORD-0000004-01.xml - short-variants )

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/ORD-0000004-01.xml \
    --experiment_info_tsv ./test/data/sample_4.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test5 - ORD-0000005-01.xml - short-variants/copy-number-alterations/rearrangements )

nextflow run main.nf \
    -profile docker,rdpc_qa,test_rdpc_qa \
    --api_token NNNNNNN \
    --xml ./test/data/ORD-0000005-01.xml \
    --experiment_info_tsv ./test/data/sample_5.tsv \
    --hg19_ref_fa /PATH/TO/hg19.fa \
    --hg19_ref_fai /PATH/TO/hg19.fa.fai \
    --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \
    --hg38_ref_fa /PATH/TO/hg38.fa.gz \
    --hg38_ref_fai /PATH/TO/hg38.fa.fai \
    --hg38_ref_dict /PATH/TO/hg38.dict