Mapping file: test/data/sample_new.tsv
XML file: test/data/example.xml
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
- Download
hg19.faandhg38.fa.gztotest/reference/ - Retrive
api_token - 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.dictTest 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.dictnextflow 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.dictnextflow 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.dictnextflow 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.dictnextflow 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.dictnextflow 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.dictnextflow 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