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##########################
nextflow \
run main.nf \
-profile docker,test,rdpc_qa \
--api_token ${qa_token} \
--xml /Users/esu/Desktop/GitHub/icgc-argo-workflows/xml_variant_ingestion/test/data/ORD-0000001-01.xml \
--experiment_info_tsv /Users/esu/Desktop/GitHub/icgc-argo-workflows/xml_variant_ingestion/test/data/sample_1.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai test/reference/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict
###SA618698
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${prod_token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-1026627-01_US0998698.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/rearrangement_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai /PATH/TO/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN
###SA618697
###IDK this rearrangement doesnt make a lot of sense b/c context is lacking
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-0886688-01_US0871226.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/rearrangementWoutChimericAnnotation_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai /PATH/TO/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN
###SA620245
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${prod_token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-0924886-01_US0906338.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/duplication_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai /PATH/TO/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN
###A620797
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${prod_token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-0925153-01.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/deletion_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai /PATH/TO/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN
###SA620407
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${prod_token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-0904928-01_US0888009.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/deletionWoutChimericAnnotation_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai test/reference/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN
###SA619843
nextflow \
run main.nf \
-profile docker,rdpc \
--api_token ${prod_token} \
--xml $HOME/Desktop/jupyter_notebooks/monstar_vcf/monstar1_f1_early_rmdup_20241101/ORD-0976156-01_US0953994.xml \
--experiment_info_tsv /Users/esu/Desktop/jupyter_notebooks/monstar_vcf/fusion_updated_metadata.tsv \
--hg19_ref_fa test/reference/hg19.fa \
--hg19_ref_fai test/reference/hg19.fa.fai \
--hg19_to_hg38_chain test/reference/hg19ToHg38.over.chain.gz \
--hg38_ref_fa test/reference/hg38.fa \
--hg38_ref_fai test/reference/hg38.fa.fai \
--hg38_ref_dict test/reference/hg38.dict \
--test_analysis_id NNNNNNNNNNN