From 73b8a1f34d29ce0a9ad1b23712ee7604a1a73462 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Wed, 17 Jul 2024 14:52:03 -0400 Subject: [PATCH] :pencil: fix spacing --- docs/SOMATIC_SNV_ANNOT_README.md | 2 +- workflows/kfdrc-somatic-snv-annot-workflow.cwl | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/SOMATIC_SNV_ANNOT_README.md b/docs/SOMATIC_SNV_ANNOT_README.md index cf9b594..adf6876 100644 --- a/docs/SOMATIC_SNV_ANNOT_README.md +++ b/docs/SOMATIC_SNV_ANNOT_README.md @@ -44,7 +44,7 @@ Secondary files needed for each reference file will be a sub-bullet point - `gatk_filter_expression`: ["vc.getGenotype('insert_normal_sample_name').getDP() <= 7", "gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER=='PASS'"] # NOTE!! Replace `insert_normal_sample_name` with the value you'd use for `input_normal_name`! # NOTE!! If your annotation includes dot values, those values must first be excluded! If they are not, GATK will error trying to convert those values! - `vep_cache`: `homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz` - `genomic_hotspots`: `tert.bed` # This file has two common TERT promoter gene hot spots - - `protein_snv_hotspots`: `protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted SNV + MNV subset of https://www.cancerhotspots.org/files/hotspots_v2.xls + - `protein_snv_hotspots`: `kfdrc_protein_snv_cancer_hotspots_20240718.txt` # Column-name-containing, tab-delimited file(s) containing protein names and amino acid positions corresponding to hotspots. File header contains generation history - `protein_indel_hotspots`: `protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted INDEL subset of https://www.cancerhotspots.org/files/hotspots_v2.xls - `custom_enst`: `kf_isoform_override.tsv` # As of VEP 104, several genes have had their canonical transcripts redefined. While the VCF will have all possible isoforms, this affects maf file output and may results in representative protein changes that defy historical expectations diff --git a/workflows/kfdrc-somatic-snv-annot-workflow.cwl b/workflows/kfdrc-somatic-snv-annot-workflow.cwl index 46cb63a..dabe64d 100644 --- a/workflows/kfdrc-somatic-snv-annot-workflow.cwl +++ b/workflows/kfdrc-somatic-snv-annot-workflow.cwl @@ -49,7 +49,7 @@ doc: | - `gatk_filter_expression`: ["vc.getGenotype('insert_normal_sample_name').getDP() <= 7", "gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER=='PASS'"] # NOTE!! Replace `insert_normal_sample_name` with the value you'd use for `input_normal_name`! # NOTE!! If your annotation includes dot values, those values must first be excluded! If they are not, GATK will error trying to convert those values! - `vep_cache`: `homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz` - `genomic_hotspots`: `tert.bed` # This file has two common TERT promoter gene hot spots - - `protein_snv_hotspots`: `protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted SNV + MNV subset of https://www.cancerhotspots.org/files/hotspots_v2.xls + - `protein_snv_hotspots`: `kfdrc_protein_snv_cancer_hotspots_20240718.txt` # A text formatted SNV + MNV version of https://www.cancerhotspots.org/files/hotspots_v2.xls. See file header for details - `protein_indel_hotspots`: `protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted INDEL subset of https://www.cancerhotspots.org/files/hotspots_v2.xls - `custom_enst`: `kf_isoform_override.tsv` # As of VEP 104, several genes have had their canonical transcripts redefined. While the VCF will have all possible isoforms, this affects maf file output and may results in representative protein changes that defy historical expectations @@ -146,7 +146,7 @@ inputs: class: File, path: 607713829360f10e3982a423, name: tert.bed}]} protein_snv_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited file(s) containing protein names and amino acid positions corresponding to hotspots", - "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6a, name: protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv}]} + "sbg:suggestedValue": [{class: File, path: 66980e845a58091951d53984, name: kfdrc_protein_snv_cancer_hotspots_20240718.txt}]} protein_indel_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited file(s) containing protein names and amino acid position ranges corresponding to hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6f,