From 25ea5783f059b0f8e68ffeb57fcdf6b108d34cd2 Mon Sep 17 00:00:00 2001 From: sophie22 Date: Wed, 13 Apr 2022 16:48:21 +0100 Subject: [PATCH 01/35] add placeholders for CNV calling input files --- egg5_config.py | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 2642893..540ee6f 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -9,7 +9,7 @@ ) assay_name = "CEN" # Core Endo Neuro -assay_version = "v1.0.3" +assay_version = "v1.1.0" ref_project_id = "project-Fkb6Gkj433GVVvj73J7x8KbV" @@ -75,6 +75,26 @@ mqc_applet_id = "app-G6FyybQ4f4xqqpFfGqg34y2Y" mqc_config_file = "{}:file-G97Jf0j433GgfGj12xKJ8Zf6".format(ref_project_id) + +# CNV calling + +cnvcall_applet_id = "applet-G9FKfxj4Z5qY6YFX155g2vQg" +cnvcalling_fixed_inputs = { + # GATK Docker image tar + "gatk_docker": "project-FzyfP204Z5qXBp6696jG5g10:file-G8KKgQQ4Z5qqk6344z2Xyq8Y", + # CEN intervals for CNV calling and its annotation + "interval_list": "file-G8p3kJQ4Gxz2BfjpJb9679j4", + "annotation_tsv": "file-G8p3kK84Gxz847Yk4XJGFjYB", + # exon annotation file + "exon_list": "file-G8y9BvQ4Z5qq7Xf67KpV5j1X" +} + +cnvcalling_input_dict = { + "app": "sentieon-dnaseq", + "patterns": ["-E '(.*).bam$'", "-E '(.*).bai$'"] +} + + # Reports xlsx_flanks = 95 From 22ef879ec32e9912f002c5ddba1b07cc908e9d9d Mon Sep 17 00:00:00 2001 From: sophie22 Date: Thu, 7 Jul 2022 13:07:03 +0100 Subject: [PATCH 02/35] update file-IDs --- egg5_config.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 540ee6f..d33848e 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -78,15 +78,13 @@ # CNV calling -cnvcall_applet_id = "applet-G9FKfxj4Z5qY6YFX155g2vQg" +cnvcall_applet_id = "applet-GByGy184xVp539QfGGf0GX86" cnvcalling_fixed_inputs = { # GATK Docker image tar - "gatk_docker": "project-FzyfP204Z5qXBp6696jG5g10:file-G8KKgQQ4Z5qqk6344z2Xyq8Y", + "gatk_docker": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GBBP9JQ433GxV97xBpQkzYZx", # CEN intervals for CNV calling and its annotation - "interval_list": "file-G8p3kJQ4Gxz2BfjpJb9679j4", - "annotation_tsv": "file-G8p3kK84Gxz847Yk4XJGFjYB", - # exon annotation file - "exon_list": "file-G8y9BvQ4Z5qq7Xf67KpV5j1X" + "interval_list": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF25v184pPF97zV91JBv0vXB", + "annotation_tsv": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF25v284pPF03q004pvvGXbf", } cnvcalling_input_dict = { From 709686564d483896e77241d8304691b2da00227f Mon Sep 17 00:00:00 2001 From: Aisha-D Date: Fri, 22 Jul 2022 12:10:59 +0100 Subject: [PATCH 03/35] rm merge conflict text --- egg5_config.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 574b690..01dc3b5 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -9,9 +9,7 @@ ) assay_name = "CEN" # Core Endo Neuro -<<<<<<< HEAD assay_version = "v1.1.5" ->>>>>>> 22ef879ec32e9912f002c5ddba1b07cc908e9d9d ref_project_id = "project-Fkb6Gkj433GVVvj73J7x8KbV" From dc19c6f051ebeb1eb2244d6e019b0fb3069e9346 Mon Sep 17 00:00:00 2001 From: AishaD Date: Fri, 22 Jul 2022 12:39:48 +0100 Subject: [PATCH 04/35] update CNV app ID --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 01dc3b5..691f5eb 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -78,7 +78,7 @@ # CNV calling -cnvcall_applet_id = "applet-GByGy184xVp539QfGGf0GX86" +cnvcall_applet_id = "app-GF3J3Kj4jq2VZkJ2P46fJ9vv" cnvcalling_fixed_inputs = { # GATK Docker image tar "gatk_docker": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GBBP9JQ433GxV97xBpQkzYZx", From ae8e891708468c577999626d7ae7535615849ce6 Mon Sep 17 00:00:00 2001 From: AishaD Date: Fri, 22 Jul 2022 13:44:28 +0100 Subject: [PATCH 05/35] rename applet to app --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 691f5eb..999e241 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -78,7 +78,7 @@ # CNV calling -cnvcall_applet_id = "app-GF3J3Kj4jq2VZkJ2P46fJ9vv" +cnvcall_app_id = "app-GF3J3Kj4jq2VZkJ2P46fJ9vv" cnvcalling_fixed_inputs = { # GATK Docker image tar "gatk_docker": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GBBP9JQ433GxV97xBpQkzYZx", From 9cb74fa15d5488c79e2cbd6009e48c751b3c9a51 Mon Sep 17 00:00:00 2001 From: AishaD Date: Fri, 19 Aug 2022 12:37:10 +0100 Subject: [PATCH 06/35] add new versions --- egg5_config.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 999e241..24aa56a 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -81,10 +81,10 @@ cnvcall_app_id = "app-GF3J3Kj4jq2VZkJ2P46fJ9vv" cnvcalling_fixed_inputs = { # GATK Docker image tar - "gatk_docker": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GBBP9JQ433GxV97xBpQkzYZx", + "gatk_docker": "{}:file-GBBP9JQ433GxV97xBpQkzYZx".format(ref_project_id), # CEN intervals for CNV calling and its annotation - "interval_list": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF25v184pPF97zV91JBv0vXB", - "annotation_tsv": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF25v284pPF03q004pvvGXbf", + "interval_list": "{}:file-GFPxzKj4V50pJX3F4vV58yyg".format(ref_project_id), + "annotation_tsv": "{}:file-GFPxzPQ4V50z4pv230p82G0q".format(ref_project_id), } cnvcalling_input_dict = { From 247c5f9b0a980844317ecbc5f3ea9baf5093d47c Mon Sep 17 00:00:00 2001 From: AishaD Date: Tue, 23 Aug 2022 15:39:27 +0100 Subject: [PATCH 07/35] GCNV-18 add reports input sections --- egg5_config.py | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/egg5_config.py b/egg5_config.py index 24aa56a..9933c41 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -191,3 +191,60 @@ "{}.exons_file ID".format(athena_stage_id): cds_file_for_athena, "{}.exons_file".format(athena_stage_id): "" } + + +# CNV Reports + +cnv_rpt_workflow_id = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:workflow-GFYvJ804qq8kBgY9BV5q2BXG" + +cnv_generate_vep_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" +cnv_annotate_excluded_regions_stage_id = "stage-GG1qYz84qq8yKzF1J2X48q62" +cnv_vep_stage_id = "stage-GFYvJF04qq8VKgq34j30pZZ3" +cnv_generate_workbook_stage_id = "stage-GFfYY9j4qq8ZxpFpP8zKG7G0" + +cnv_vep_config = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GFBgJg84xVp3X4q3BX7jXbbZ " + +cnv_rpt_stage_input_dict = { + # generate_bed + "{}.sample_file".format(cnv_generate_vep_stage_id): { + "app": "mosdepth", "subdir": "", + "pattern": "-E '{}(.*).per-base.bed.gz.csi$'" + }, + # vep + "{}.vcf".format(cnv_vep_stage_id): { + "app": "sentieon-dnaseq", "subdir": "", + "pattern": "-E '{}(.*)[^g].vcf.gz$'" + } +} + +rpt_dynamic_files = { + # inputs for generate bed for vep + "{}.exons_nirvana ID".format(cnv_generate_vep_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_vep_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_vep_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_vep_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_vep_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_vep_stage_id): "", + "{}.manifest ID".format(cnv_generate_vep_stage_id): bioinformatic_manifest, + "{}.manifest".format(cnv_generate_vep_stage_id): "" +} + +# CNV reanalysis + +rea_stage_input_dict = { + # vep + "{}.vcf".format(cnv_vep_stage_id): { + "app": "sentieon-dnaseq", "subdir": "", + "pattern": "-E '{}(.*)[^g].vcf.gz$'" + }, +} + +rea_dynamic_files = { + # inputs for generate bed for vep + "{}.exons_nirvana ID".format(cnv_generate_vep_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_vep_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_vep_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_vep_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_vep_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_vep_stage_id): "" +} From 6a52911cb0cbef30aa2e79d53eecbd37ba7b74ed Mon Sep 17 00:00:00 2001 From: AishaD Date: Fri, 26 Aug 2022 17:47:24 +0100 Subject: [PATCH 08/35] update stage IDs --- egg5_config.py | 45 ++++++++++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 19 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 9933c41..53658db 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -197,7 +197,9 @@ cnv_rpt_workflow_id = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:workflow-GFYvJ804qq8kBgY9BV5q2BXG" -cnv_generate_vep_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" + +cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" +cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" cnv_annotate_excluded_regions_stage_id = "stage-GG1qYz84qq8yKzF1J2X48q62" cnv_vep_stage_id = "stage-GFYvJF04qq8VKgq34j30pZZ3" cnv_generate_workbook_stage_id = "stage-GFfYY9j4qq8ZxpFpP8zKG7G0" @@ -206,7 +208,7 @@ cnv_rpt_stage_input_dict = { # generate_bed - "{}.sample_file".format(cnv_generate_vep_stage_id): { + "{}.sample_file".format(cnv_generate_bed_vep_stage_id): { "app": "mosdepth", "subdir": "", "pattern": "-E '{}(.*).per-base.bed.gz.csi$'" }, @@ -214,24 +216,29 @@ "{}.vcf".format(cnv_vep_stage_id): { "app": "sentieon-dnaseq", "subdir": "", "pattern": "-E '{}(.*)[^g].vcf.gz$'" + }, + # excluded_annotate + "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { + "app": "eggd_GATKgCNV_call", "subdir": "", + "pattern": "-E '(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } -rpt_dynamic_files = { +cnv_rpt_dynamic_files = { # inputs for generate bed for vep - "{}.exons_nirvana ID".format(cnv_generate_vep_stage_id): cds_file, - "{}.exons_nirvana".format(cnv_generate_vep_stage_id): "", - "{}.nirvana_genes2transcripts ID".format(cnv_generate_vep_stage_id): genes2transcripts, - "{}.nirvana_genes2transcripts".format(cnv_generate_vep_stage_id): "", - "{}.gene_panels ID".format(cnv_generate_vep_stage_id): genepanels_file, - "{}.gene_panels".format(cnv_generate_vep_stage_id): "", - "{}.manifest ID".format(cnv_generate_vep_stage_id): bioinformatic_manifest, - "{}.manifest".format(cnv_generate_vep_stage_id): "" + "{}.exons_nirvana ID".format(cnv_generate_bed_vep_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_bed_vep_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_bed_vep_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_bed_vep_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_bed_vep_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_bed_vep_stage_id): "", + "{}.manifest ID".format(cnv_generate_bed_vep_stage_id): bioinformatic_manifest, + "{}.manifest".format(cnv_generate_bed_vep_stage_id): "" } # CNV reanalysis -rea_stage_input_dict = { +cnv_rea_stage_input_dict = { # vep "{}.vcf".format(cnv_vep_stage_id): { "app": "sentieon-dnaseq", "subdir": "", @@ -239,12 +246,12 @@ }, } -rea_dynamic_files = { +cvn_rea_dynamic_files = { # inputs for generate bed for vep - "{}.exons_nirvana ID".format(cnv_generate_vep_stage_id): cds_file, - "{}.exons_nirvana".format(cnv_generate_vep_stage_id): "", - "{}.nirvana_genes2transcripts ID".format(cnv_generate_vep_stage_id): genes2transcripts, - "{}.nirvana_genes2transcripts".format(cnv_generate_vep_stage_id): "", - "{}.gene_panels ID".format(cnv_generate_vep_stage_id): genepanels_file, - "{}.gene_panels".format(cnv_generate_vep_stage_id): "" + "{}.exons_nirvana ID".format(cnv_generate_bed_vep_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_bed_vep_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_bed_vep_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_bed_vep_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_bed_vep_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_bed_vep_stage_id): "" } From 48353738ea49d3c48cfc3b91894a82d53b32f273 Mon Sep 17 00:00:00 2001 From: AishaD Date: Tue, 30 Aug 2022 16:55:44 +0100 Subject: [PATCH 09/35] add generate bed for excluded app inputs --- egg5_config.py | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 53658db..599c27d 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -233,7 +233,16 @@ "{}.gene_panels ID".format(cnv_generate_bed_vep_stage_id): genepanels_file, "{}.gene_panels".format(cnv_generate_bed_vep_stage_id): "", "{}.manifest ID".format(cnv_generate_bed_vep_stage_id): bioinformatic_manifest, - "{}.manifest".format(cnv_generate_bed_vep_stage_id): "" + "{}.manifest".format(cnv_generate_bed_vep_stage_id): "", + # inputs for generate bed for excluded app + "{}.exons_nirvana ID".format(cnv_generate_bed_excluded_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_bed_excluded_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_bed_excluded_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_bed_excluded_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_bed_excluded_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_bed_excluded_stage_id): "", + "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, + "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "" } # CNV reanalysis @@ -253,5 +262,14 @@ "{}.nirvana_genes2transcripts ID".format(cnv_generate_bed_vep_stage_id): genes2transcripts, "{}.nirvana_genes2transcripts".format(cnv_generate_bed_vep_stage_id): "", "{}.gene_panels ID".format(cnv_generate_bed_vep_stage_id): genepanels_file, - "{}.gene_panels".format(cnv_generate_bed_vep_stage_id): "" + "{}.gene_panels".format(cnv_generate_bed_vep_stage_id): "", + # inputs for generate bed for excluded app + "{}.exons_nirvana ID".format(cnv_generate_bed_excluded_stage_id): cds_file, + "{}.exons_nirvana".format(cnv_generate_bed_excluded_stage_id): "", + "{}.nirvana_genes2transcripts ID".format(cnv_generate_bed_excluded_stage_id): genes2transcripts, + "{}.nirvana_genes2transcripts".format(cnv_generate_bed_excluded_stage_id): "", + "{}.gene_panels ID".format(cnv_generate_bed_excluded_stage_id): genepanels_file, + "{}.gene_panels".format(cnv_generate_bed_excluded_stage_id): "", + "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, + "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "" } From c75b6272020f4f8deb3af3e6ad7a4e4023231cf6 Mon Sep 17 00:00:00 2001 From: AishaD Date: Tue, 30 Aug 2022 17:40:54 +0100 Subject: [PATCH 10/35] add cds inputs --- egg5_config.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 599c27d..c1abad5 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -197,7 +197,6 @@ cnv_rpt_workflow_id = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:workflow-GFYvJ804qq8kBgY9BV5q2BXG" - cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" cnv_annotate_excluded_regions_stage_id = "stage-GG1qYz84qq8yKzF1J2X48q62" @@ -242,7 +241,10 @@ "{}.gene_panels ID".format(cnv_generate_bed_excluded_stage_id): genepanels_file, "{}.gene_panels".format(cnv_generate_bed_excluded_stage_id): "", "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, - "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "" + "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "", + # inputs for excluded app + "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): cds_file, + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena } # CNV reanalysis From 7ce1100cb062c60b4e7b34fe0e930571e12715ca Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 10:14:32 +0100 Subject: [PATCH 11/35] have ID columns --- egg5_config.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index c1abad5..8d0a0ee 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -243,8 +243,10 @@ "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "", # inputs for excluded app - "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): cds_file, - "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena + "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, + "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", + "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena, + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "", } # CNV reanalysis From 8d50c24e591f02fa1d0aaa21575cdf104bb7c6a4 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 10:46:29 +0100 Subject: [PATCH 12/35] get excluded files --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 8d0a0ee..0674d54 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -219,7 +219,7 @@ # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "", - "pattern": "-E '(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" + "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } From b71a546c1124d7a60fe99344e84f0aa802045935 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 10:59:41 +0100 Subject: [PATCH 13/35] add subdirectory --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 0674d54..5267f7d 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -218,7 +218,7 @@ }, # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "", + "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } From fef1e7bd5c236cecb788c00b580df48d989a6f6c Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 11:22:31 +0100 Subject: [PATCH 14/35] rm brackets --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 5267f7d..7e24251 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -219,7 +219,7 @@ # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", - "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" + "pattern": "-E '(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } From a8672e557dcd1f41835d8f5588f9062a2e405546 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 11:43:22 +0100 Subject: [PATCH 15/35] pont for CNV vcfs --- egg5_config.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 7e24251..7028c3e 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -213,8 +213,8 @@ }, # vep "{}.vcf".format(cnv_vep_stage_id): { - "app": "sentieon-dnaseq", "subdir": "", - "pattern": "-E '{}(.*)[^g].vcf.gz$'" + "app": "eggd_GATKgCNV_call", "subdir": "", + "pattern": "-E '{}(.*)[^g]_segments.vcf.gz$'" }, # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { From 6cb680c83a0a48512523e954f0a481187f70542d Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 11:55:03 +0100 Subject: [PATCH 16/35] return the brackets --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 7028c3e..a309cd2 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -219,7 +219,7 @@ # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", - "pattern": "-E '(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" + "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } From 8e6a8d2cf784059bd580ef99810b99c6c5217333 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 12:18:17 +0100 Subject: [PATCH 17/35] return sundir --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index a309cd2..0e6b8f0 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -218,7 +218,7 @@ }, # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", + "app": "eggd_GATKgCNV_call", "subdir": "", "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" } } From 03259ce2ea12490c43d6d1dbfa286c6857ceff6e Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 12:31:17 +0100 Subject: [PATCH 18/35] add comma --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 0e6b8f0..56b2ac2 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -220,7 +220,7 @@ "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "", "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" - } + }, } cnv_rpt_dynamic_files = { From 4b21648407a01465e39e0b342977a58ab2cfc0f3 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 14:24:14 +0100 Subject: [PATCH 19/35] add mosdepth input for generae bed --- egg5_config.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 56b2ac2..3ab9854 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -206,11 +206,16 @@ cnv_vep_config = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GFBgJg84xVp3X4q3BX7jXbbZ " cnv_rpt_stage_input_dict = { - # generate_bed + # generate_bed for vep generate bed "{}.sample_file".format(cnv_generate_bed_vep_stage_id): { "app": "mosdepth", "subdir": "", "pattern": "-E '{}(.*).per-base.bed.gz.csi$'" }, + # generate_bed for excluded generate bed + "{}.sample_file".format(cnv_generate_bed_excluded_stage_id): { + "app": "mosdepth", "subdir": "", + "pattern": "-E '{}(.*).per-base.bed.gz.csi$'" + }, # vep "{}.vcf".format(cnv_vep_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "", @@ -219,7 +224,7 @@ # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "", - "pattern": "-E '{}(.*)_CNV_dias_batch_integration_excluded_intervals.bed$'" + "pattern": "-E '{}(.*)excluded_intervals.bed$'" }, } From d38c9e48fffa3537831b44d041fe2b013e4afac5 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 31 Aug 2022 14:30:01 +0100 Subject: [PATCH 20/35] update reanalysis dict --- egg5_config.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 3ab9854..825459d 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -251,19 +251,23 @@ "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena, - "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "", + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "" } # CNV reanalysis -cnv_rea_stage_input_dict = { +cnv_rea_stage_input_dict = { # vep "{}.vcf".format(cnv_vep_stage_id): { - "app": "sentieon-dnaseq", "subdir": "", - "pattern": "-E '{}(.*)[^g].vcf.gz$'" + "app": "eggd_GATKgCNV_call", "subdir": "", + "pattern": "-E '{}(.*)[^g]_segments.vcf.gz$'" + }, + # excluded_annotate + "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { + "app": "eggd_GATKgCNV_call", "subdir": "", + "pattern": "-E '{}(.*)excluded_intervals.bed$'" }, } - cvn_rea_dynamic_files = { # inputs for generate bed for vep "{}.exons_nirvana ID".format(cnv_generate_bed_vep_stage_id): cds_file, From fec37dd42ae120d724c49bb4da3a9e3b4fb9dd6e Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 1 Sep 2022 13:01:34 +0100 Subject: [PATCH 21/35] add subdirs --- egg5_config.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 825459d..262578e 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -218,13 +218,13 @@ }, # vep "{}.vcf".format(cnv_vep_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "", + "app": "eggd_GATKgCNV_call", "subdir": "CNV_vcfs", "pattern": "-E '{}(.*)[^g]_segments.vcf.gz$'" }, # excluded_annotate "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "", - "pattern": "-E '{}(.*)excluded_intervals.bed$'" + "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", + "pattern": "-E '{}(.*)_excluded_intervals.bed$'" }, } From 3d455a071b34dea66b3b67b4c94f63c109d084f4 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 1 Sep 2022 14:01:29 +0100 Subject: [PATCH 22/35] add backward dashs --- egg5_config.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 262578e..245532b 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -217,13 +217,15 @@ "pattern": "-E '{}(.*).per-base.bed.gz.csi$'" }, # vep + # subdirectories always require the backward dash "{}.vcf".format(cnv_vep_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "CNV_vcfs", - "pattern": "-E '{}(.*)[^g]_segments.vcf.gz$'" + "app": "eggd_GATKgCNV_call", "subdir": "CNV_vcfs/", + "pattern": "-E '{}(.*)_segments.vcf$'" }, # excluded_annotate + # subdirectories always require the backward dash "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary", + "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary/", "pattern": "-E '{}(.*)_excluded_intervals.bed$'" }, } From 14fced9b4c64c88b05b9b4da93fe87271aabb8c1 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 1 Sep 2022 14:29:46 +0100 Subject: [PATCH 23/35] rm brackets for excluded regions file --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 245532b..65579ed 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -226,7 +226,7 @@ # subdirectories always require the backward dash "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary/", - "pattern": "-E '{}(.*)_excluded_intervals.bed$'" + "pattern": "-E '(.*)_excluded_intervals.bed$'" }, } From f49246cabbb2ebc2c61377fe6815ad1b3f598389 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 1 Sep 2022 17:43:15 +0100 Subject: [PATCH 24/35] update cnv reanalysis --- egg5_config.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/egg5_config.py b/egg5_config.py index 65579ed..a31a65c 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -260,14 +260,16 @@ cnv_rea_stage_input_dict = { # vep + # subdirectories always require the backward dash "{}.vcf".format(cnv_vep_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "", - "pattern": "-E '{}(.*)[^g]_segments.vcf.gz$'" + "app": "eggd_GATKgCNV_call", "subdir": "CNV_vcfs/", + "pattern": "-E '{}(.*)_segments.vcf$'" }, # excluded_annotate + # subdirectories always require the backward dash "{}.excluded_regions".format(cnv_annotate_excluded_regions_stage_id): { - "app": "eggd_GATKgCNV_call", "subdir": "", - "pattern": "-E '{}(.*)excluded_intervals.bed$'" + "app": "eggd_GATKgCNV_call", "subdir": "CNV_summary/", + "pattern": "-E '(.*)_excluded_intervals.bed$'" }, } cvn_rea_dynamic_files = { @@ -286,5 +288,10 @@ "{}.gene_panels ID".format(cnv_generate_bed_excluded_stage_id): genepanels_file, "{}.gene_panels".format(cnv_generate_bed_excluded_stage_id): "", "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, - "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "" + "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "", + # inputs for excluded app + "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, + "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", + "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena, + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "" } From 11d5acc70cf737c1a09b1f4a639a7912df2f83bc Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 1 Sep 2022 17:57:41 +0100 Subject: [PATCH 25/35] fix typo --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index a31a65c..0769ac2 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -272,7 +272,7 @@ "pattern": "-E '(.*)_excluded_intervals.bed$'" }, } -cvn_rea_dynamic_files = { +cnv_rea_dynamic_files = { # inputs for generate bed for vep "{}.exons_nirvana ID".format(cnv_generate_bed_vep_stage_id): cds_file, "{}.exons_nirvana".format(cnv_generate_bed_vep_stage_id): "", From c65150ea651f394fafbcca199fa489d245a08c50 Mon Sep 17 00:00:00 2001 From: AishaD Date: Fri, 9 Sep 2022 11:42:25 +0100 Subject: [PATCH 26/35] Update cnv reports workflow to publsihed ones --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 0769ac2..a1ab663 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -195,7 +195,7 @@ # CNV Reports -cnv_rpt_workflow_id = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:workflow-GFYvJ804qq8kBgY9BV5q2BXG" +cnv_rpt_workflow_id = "{}:workflow-GGJ24y0433GVFkXGG6bBvV35".format(ref_project_id) cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" From a57057f4d9f86edc092cd3c8727813e9a8da7ea0 Mon Sep 17 00:00:00 2001 From: AishaD Date: Mon, 12 Sep 2022 14:34:18 +0100 Subject: [PATCH 27/35] add additional files --- egg5_config.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index a1ab663..89211be 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -204,6 +204,7 @@ cnv_generate_workbook_stage_id = "stage-GFfYY9j4qq8ZxpFpP8zKG7G0" cnv_vep_config = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GFBgJg84xVp3X4q3BX7jXbbZ " +additional_regions = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GG4J0P04qq8QJjKKFv68yzGX" cnv_rpt_stage_input_dict = { # generate_bed for vep generate bed @@ -253,7 +254,9 @@ "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena, - "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "" + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "", + "{}.additional_regions ID".format(cnv_annotate_excluded_regions_stage_id): additional_regions, + "{}.additional_regions".format(cnv_annotate_excluded_regions_stage_id): "" } # CNV reanalysis From 73835594b0eb7990214539b1da8cf4e5f4daf7fb Mon Sep 17 00:00:00 2001 From: AishaD Date: Mon, 12 Sep 2022 15:06:14 +0100 Subject: [PATCH 28/35] add additional files to cnvreanalysis --- egg5_config.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 89211be..a29b1f8 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -296,5 +296,7 @@ "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena, - "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "" + "{}.cds_gene".format(cnv_annotate_excluded_regions_stage_id): "", + "{}.additional_regions ID".format(cnv_annotate_excluded_regions_stage_id): additional_regions, + "{}.additional_regions".format(cnv_annotate_excluded_regions_stage_id): "" } From eab36d4e9cc339e367489f2199921f6b14ee7875 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 28 Sep 2022 12:08:04 +0100 Subject: [PATCH 29/35] update CNV reports workflow draft v1.0.1 --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index a29b1f8..2214575 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -195,7 +195,7 @@ # CNV Reports -cnv_rpt_workflow_id = "{}:workflow-GGJ24y0433GVFkXGG6bBvV35".format(ref_project_id) +cnv_rpt_workflow_id = "project-GGp20VQ4Qpk62Kjx4gX6kvkP:workflow-GGp2FbQ4QpkJ856z4k9Q8J7q" cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" From 979505a6fe6ee820ef2b51e4f1ece0df90d01b1a Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 28 Sep 2022 12:11:43 +0100 Subject: [PATCH 30/35] add v1.0.0 of cnv vep config file --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 2214575..54dc901 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -203,7 +203,7 @@ cnv_vep_stage_id = "stage-GFYvJF04qq8VKgq34j30pZZ3" cnv_generate_workbook_stage_id = "stage-GFfYY9j4qq8ZxpFpP8zKG7G0" -cnv_vep_config = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GFBgJg84xVp3X4q3BX7jXbbZ " +cnv_vep_config = "{}:file-GGkJqk84GVVGqG6VFz60gkFF".format(ref_project_id) additional_regions = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GG4J0P04qq8QJjKKFv68yzGX" cnv_rpt_stage_input_dict = { From 48d20330125b7df4e4fb617374eed4d024b58beb Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 28 Sep 2022 13:17:13 +0100 Subject: [PATCH 31/35] use live addtional v1.0.0 --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 54dc901..2066d47 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -204,7 +204,7 @@ cnv_generate_workbook_stage_id = "stage-GFfYY9j4qq8ZxpFpP8zKG7G0" cnv_vep_config = "{}:file-GGkJqk84GVVGqG6VFz60gkFF".format(ref_project_id) -additional_regions = "project-GFQQyVQ4qq8j6kXG1Xkfy3G3:file-GG4J0P04qq8QJjKKFv68yzGX" +additional_regions = "{}:file-GGkz5B84GVV4KbX64gzBXqZ2".format(ref_project_id) cnv_rpt_stage_input_dict = { # generate_bed for vep generate bed From 1df78ce2b8db52e05447923449d8a165a40ad872 Mon Sep 17 00:00:00 2001 From: AishaD Date: Wed, 28 Sep 2022 15:38:32 +0100 Subject: [PATCH 32/35] use corrected workflow v1.0.1 --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 2066d47..18c0501 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -195,7 +195,7 @@ # CNV Reports -cnv_rpt_workflow_id = "project-GGp20VQ4Qpk62Kjx4gX6kvkP:workflow-GGp2FbQ4QpkJ856z4k9Q8J7q" +cnv_rpt_workflow_id = "project-GGp20VQ4Qpk62Kjx4gX6kvkP:workflow-GGp5jK04Qpk9Qp9Q4fBK0pfF" cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" From 8a45df8f2ef608b5da2d4f49ebc432462b85a8c9 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 29 Sep 2022 14:32:48 +0100 Subject: [PATCH 33/35] update version --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 18c0501..5e89f2c 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -9,7 +9,7 @@ ) assay_name = "CEN" # Core Endo Neuro -assay_version = "v1.1.5" +assay_version = "v1.2.0" ref_project_id = "project-Fkb6Gkj433GVVvj73J7x8KbV" From eeee05ee1ae539349d1336252bab56dba40b9aa5 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 29 Sep 2022 14:46:25 +0100 Subject: [PATCH 34/35] update to published v1.0.1 rpt workflow --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 5e89f2c..3d06f3b 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -195,7 +195,7 @@ # CNV Reports -cnv_rpt_workflow_id = "project-GGp20VQ4Qpk62Kjx4gX6kvkP:workflow-GGp5jK04Qpk9Qp9Q4fBK0pfF" +cnv_rpt_workflow_id = "{}:workflow-GGpkk40433GQqXQj4j2FyV36".format(ref_project_id) cnv_generate_bed_excluded_stage_id = "stage-GFZQB7Q4qq8X6yjKG2pFQ58x" cnv_generate_bed_vep_stage_id = "stage-GG39Gq04qq8ZkfgV31yQy93v" From 677eff7965c527938a036ed13ce335ed2fa138d8 Mon Sep 17 00:00:00 2001 From: AishaD Date: Thu, 29 Sep 2022 14:47:02 +0100 Subject: [PATCH 35/35] rm ws --- egg5_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/egg5_config.py b/egg5_config.py index 3d06f3b..379ca24 100644 --- a/egg5_config.py +++ b/egg5_config.py @@ -292,7 +292,7 @@ "{}.gene_panels".format(cnv_generate_bed_excluded_stage_id): "", "{}.manifest ID".format(cnv_generate_bed_excluded_stage_id): bioinformatic_manifest, "{}.manifest".format(cnv_generate_bed_excluded_stage_id): "", - # inputs for excluded app + # inputs for excluded app "{}.cds_hgnc ID".format(cnv_annotate_excluded_regions_stage_id): cds_file, "{}.cds_hgnc".format(cnv_annotate_excluded_regions_stage_id): "", "{}.cds_gene ID".format(cnv_annotate_excluded_regions_stage_id): cds_file_for_athena,