Note: There are too many changes for GitHub to recognise the JSON as the same file after renaming (no pretty diff) so I created a branch (_DI-700v3.1.0) to rename the JSON then branched from there to make changes (v3.1.0_changes) - the DI-700_v3.1.0 branch can then be merged to main later.
Changes
Rename file from v3.0.3 → v3.1.0
Update artemis app ID from app-GZ1X5zj4K5ZxyfYPPq4YgGv3 (v1.3.0) → app-GfKV5204ZF35Z47z31Qzqx90 (v1.4.0)
Update SNV reports workflow to v2.2.0
Update CNV reports workflow to v1.2.0
Update genepanels and g2t file IDs to newer versions
cnv_reports
stage-cnv_generate_bed_vep
Update input names for eggd_generate_bed (exons_nirvana -> exons and nirvana_genes2transcripts -> genes2transcripts) which affects:
stage-cnv_generate_bed_vep
stage-cnv_generate_bed_excluded
Add new string inputs which work with new eggd_dias_batch (v3.1.0) which affects:
stage-cnv_generate_bed_vep
stage-cnv_generate_bed_excluded
stage-cnv_generate_workbook
stage-cnv_generate_workbook
Update acmg from true -> 3
Add new input lock_sheet set to true
snv_reports and mosaic_reports
Update input names for eggd_generate_bed (exons_nirvana -> exons and nirvana_genes2transcripts -> genes2transcripts) which affects:
stage-rpt_generate_bed_athena
stage-rpt_generate_bed_vep
stage-rpt_generate_workbook
Add new string inputs which work with new eggd_dias_batch (v3.1.0) which affects:
stage-rpt_generate_bed_athena
stage-rpt_generate_bed_vep
stage-rpt_generate_workbook
stage-rpt_athena
stage-rpt_vep
Update VEP config file ID cen_vep_config_v1.1.11.json -> cen_vep_config_v1.1.12.json
Add inputs for new app eggd_optimised_filtering
stage-rpt_generate_workbook
Remove CSQ_gnomADg_AF_popmax and CSQ_gnomADe_AF_popmax from exclude_columns because they're now used for filtering
Update acmg from true -> 3
Update filter to just filter out EXCLUDE variants since filtering now done within eggd_optimised_filtering
Update human_filter to reflect new filtering
Update reorder_columns to include CSQ_gnomADg_AF_popmax, CSQ_gnomADe_AF_popmax and MOI
Add new input lock_sheet set to true
stage-rpt_athena
Add new input indication
README
Update title dias_CEN_config_GRCh37_v3.0.3.json -> dias_CEN_config_GRCh37_v3.1.0.json
Update link to eggd_dias_batch from https://github.com/eastgenomics/dias_batch_running → https://github.com/eastgenomics/eggd_dias_batch
Update Dias reports version and ID dias_reports_v2.1.0 and workflow-GXzkfYj4QPQp9z4Jz4BF09y6 -> dias_reports_v2.2.0 and workflow-Gg9Yvj04z4VvPFF3fygp63jy
Update Dias CNV reports workflow version and ID dias_cnvreports_v1.1.0 and workflow-GXzvJq84XZB1fJk9fBfG88XJ -> dias_cnvreports_v1.2.0 and workflow-Gg9Ybq841Ky1xfYgQ2qjqG3F
Update artemis version and app ID v1.3.0 (app-GZ1X5zj4K5ZxyfYPPq4YgGv3) -> v1.4.0 (app-GfKV5204ZF35Z47z31Qzqx90)
Update dynamic files genepanels, genes2transcripts, cen_vep_config for SNV/mosaic reports names and IDs and add panel_dump
Note: There are too many changes for GitHub to recognise the JSON as the same file after renaming (no pretty diff) so I created a branch (_DI-700v3.1.0) to rename the JSON then branched from there to make changes (v3.1.0_changes) - the DI-700_v3.1.0 branch can then be merged to main later.
Changes
app-GZ1X5zj4K5ZxyfYPPq4YgGv3(v1.3.0) →app-GfKV5204ZF35Z47z31Qzqx90(v1.4.0)acmgfrom true -> 3lock_sheetset to trueCSQ_gnomADg_AF_popmaxandCSQ_gnomADe_AF_popmaxfrom exclude_columns because they're now used for filteringacmgfrom true -> 3filterto just filter out EXCLUDE variants since filtering now done within eggd_optimised_filteringhuman_filterto reflect new filteringreorder_columnsto includeCSQ_gnomADg_AF_popmax,CSQ_gnomADe_AF_popmaxandMOIlock_sheetset to trueindicationREADME
dias_CEN_config_GRCh37_v3.0.3.json->dias_CEN_config_GRCh37_v3.1.0.jsonhttps://github.com/eastgenomics/dias_batch_running→https://github.com/eastgenomics/eggd_dias_batchdias_reports_v2.1.0andworkflow-GXzkfYj4QPQp9z4Jz4BF09y6->dias_reports_v2.2.0andworkflow-Gg9Yvj04z4VvPFF3fygp63jydias_cnvreports_v1.1.0andworkflow-GXzvJq84XZB1fJk9fBfG88XJ->dias_cnvreports_v1.2.0andworkflow-Gg9Ybq841Ky1xfYgQ2qjqG3Fapp-GZ1X5zj4K5ZxyfYPPq4YgGv3) -> v1.4.0 (app-GfKV5204ZF35Z47z31Qzqx90)Testing The config was upload to DNAnexus (https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/data/?scope=project&id.values=file-GgG94Jj4z4VVF2bGQpX4K4bk) and used as an input to Dias batch v3.1.0 to run SNV reports, CNV reports and artemis for two CEN samples: Dias batch job https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/job/GgG95084z4VkVX3b261Fk31y SNV reports jobs https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/analysis/GgG95Y04z4VbPzgjJQvx4xx0 https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/analysis/GgG95YQ4z4Vq3yxP24b3GxJy CNV reports jobs https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/analysis/GgG95Qj4z4VQ6Yqp9FjjV3pX https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/analysis/GgG95Vj4z4VgV2xpFkB1jXGp artemis https://platform.dnanexus.com/panx/projects/Gg5Z9VQ4z4Vz8G64byYQbXb6/monitor/job/GgG95Z04z4VZjXZG0bf63QPg
Documentation so far: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3112960008/dias+CEN+config+GRCh37+v3.1.0.json
This change is