New WDL to create VAT tsvs from previously generated BigQuery table. #8165
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8165 +/- ##
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Coverage ? 86.215%
Complexity ? 35195
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Files ? 2173
Lines ? 165045
Branches ? 17793
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Hits ? 142293
Misses ? 16420
Partials ? 6332 |
mcovarr
approved these changes
Jan 19, 2023
scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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| File monitoring_script = "gs://gvs_quickstart_storage/cromwell_monitoring_script.sh" | ||
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| # going large with the default to make gsutil -m cp really zippy |
scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
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| echo "vid transcript contig position ref_allele alt_allele gvs_all_ac gvs_all_an gvs_all_af gvs_all_sc gvs_max_af gvs_max_ac gvs_max_an gvs_max_sc gvs_max_subpop gvs_afr_ac gvs_afr_an gvs_afr_af gvs_afr_sc gvs_amr_ac gvs_amr_an gvs_amr_af gvs_amr_sc gvs_eas_ac gvs_eas_an gvs_eas_af gvs_eas_sc gvs_eur_ac gvs_eur_an gvs_eur_af gvs_eur_sc gvs_mid_ac gvs_mid_an gvs_mid_af gvs_mid_sc gvs_oth_ac gvs_oth_an gvs_oth_af gvs_oth_sc gvs_sas_ac gvs_sas_an gvs_sas_af gvs_sas_sc gene_symbol transcript_source aa_change consequence dna_change_in_transcript variant_type exon_number intron_number genomic_location dbsnp_rsid gene_id gene_omim_id is_canonical_transcript gnomad_all_af gnomad_all_ac gnomad_all_an gnomad_failed_filter gnomad_max_af gnomad_max_ac gnomad_max_an gnomad_max_subpop gnomad_afr_ac gnomad_afr_an gnomad_afr_af gnomad_amr_ac gnomad_amr_an gnomad_amr_af gnomad_asj_ac gnomad_asj_an gnomad_asj_af gnomad_eas_ac gnomad_eas_an gnomad_eas_af gnomad_fin_ac gnomad_fin_an gnomad_fin_af gnomad_nfr_ac gnomad_nfr_an gnomad_nfr_af gnomad_sas_ac gnomad_sas_an gnomad_sas_af gnomad_oth_ac gnomad_oth_an gnomad_oth_af revel splice_ai_acceptor_gain_score splice_ai_acceptor_gain_distance splice_ai_acceptor_loss_score splice_ai_acceptor_loss_distance splice_ai_donor_gain_score splice_ai_donor_gain_distance splice_ai_donor_loss_score splice_ai_donor_loss_distance omim_phenotypes_id omim_phenotypes_name clinvar_classification clinvar_last_updated clinvar_phenotype" | gzip > header.gz | ||
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| echo_date "concatenating $files" | ||
| cat $(echo $files) > vat_complete.tsv.gz |
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this is still magical to me 🪄
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Yeah, same. I just copied it. 🤷
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Successful run of GvsCreateVATFilesFromBigQuery here: https://app.terra.bio/#workspaces/gvs-dev/GVS%20Quickstart%20v3%20ggrant/job_history/dfeea2fc-22eb-41d1-8342-a971572aba4d Successful run of GvsCreateVATFromVDS here: https://app.terra.bio/#workspaces/gvs-dev/GVS%20Quickstart%20v3%20ggrant/job_history/4b83a498-5bd8-4f42-b312-1d0efcf55cfc |
Miguel's additions. Co-authored-by: Miguel Covarrubias <[email protected]>
Error in query string: Error processing job 'gvs- internal:bqjob_r171d52c52c0d6fcf_00000185cbfc3198_1': DREMEL only supports single character delimiters. Cannot use "tab"
RoriCremer
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that referenced
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Jan 31, 2023
This was referenced Mar 17, 2023
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