From a9526ddaa5e926a397e5f618e63e91cc4d3c86a6 Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Mon, 28 Oct 2024 10:42:18 -0700 Subject: [PATCH] Update reference paths --- README.md | 4 ++-- config/template.config | 12 ++++++------ test/config/ssv-all-tools.config | 4 ++-- test/config/ssv-delly.config | 4 ++-- test/config/ssv-manta.config | 4 ++-- test/configtest-F16.json | 4 ++-- 6 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 953378e..5106663 100644 --- a/README.md +++ b/README.md @@ -137,8 +137,8 @@ input: | dataset_id | yes | string | Boutros Lab dataset id | | blcds_registered_dataset | yes | boolean | Affirms if dataset should be registered in the Boutros Lab Data registry. Default value is `false`. | | algorithm | yes | list | List containing a combination of SV callers `delly`, `manta`. List can contain a single caller of choice. | -| reference_fasta | yes | path | Absolute path to the reference genome FASTA file. The reference genome is used by Delly for structural variant calling. GRCh37 - /hot/ref/reference/GRCh37-EBI-hs37d5/hs37d5.fa, GRCh38 - /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta | -| exclusion_file | yes | path | Absolute path to the Delly reference genome exclusion file utilized to remove suggested regions for structural variant calling. GRCh37 - /hot/ref/tool-specific-input/Delly/GRCh37-EBI-hs37d/human.hs37d5.excl.tsv, GRCh38 - /hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv | +| reference_fasta | yes | path | Absolute path to the reference genome FASTA file. The reference genome is used by Delly for structural variant calling. GRCh37 - /hot/resource/reference-genome/GRCh37-EBI-hs37d5/hs37d5.fa, GRCh38 - /hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta | +| exclusion_file | yes | path | Absolute path to the Delly reference genome exclusion file utilized to remove suggested regions for structural variant calling. GRCh37 - /hot/resource/tool-specific-input/Delly/GRCh37-EBI-hs37d/human.hs37d5.excl.tsv, GRCh38 - /hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv | | map_qual | yes | integer | Minimum paired-end (PE) mapping quality (MAPQ) for Delly. Default set to 20.| | min_clique_size | yes | integer | Minimum number of supporting PE or split-read (SR) alignments required for a clique to be identified as a structural variant by Delly. Adjust this parameter to control the sensitivity and specificity of Delly variant calling. Default set to 5.| | mad_cutoff | yes | integer | Insert size cutoff, median+s*MAD (deletions only) for Delly. Default set to 15.| diff --git a/config/template.config b/config/template.config index a58bcf3..6971113 100755 --- a/config/template.config +++ b/config/template.config @@ -11,13 +11,13 @@ params { blcds_registered_dataset = false - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" - // GRCh37 blacklist - /hot/ref/tool-specific-input/GRIDSS-2.13.2/GRCh37-EBI-hs37d5/ENCFF001TDO.bed - // GRCh38 blacklist - /hot/ref/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed - gridss_blacklist = "/hot/ref/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed" - gridss_reference_fasta = "/hot/ref/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + // GRCh37 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh37-EBI-hs37d5/ENCFF001TDO.bed + // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed + gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed" + gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" - exclusion_file = "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" + exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" output_dir = "where/to/save/outputs/" diff --git a/test/config/ssv-all-tools.config b/test/config/ssv-all-tools.config index 17d1c2c..a722cea 100644 --- a/test/config/ssv-all-tools.config +++ b/test/config/ssv-all-tools.config @@ -11,9 +11,9 @@ params { blcds_registered_dataset = false - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" - exclusion_file = "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" + exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" // select the tool(s) to run algorithm = ['delly', 'manta'] diff --git a/test/config/ssv-delly.config b/test/config/ssv-delly.config index 0dc972f..d0b111b 100644 --- a/test/config/ssv-delly.config +++ b/test/config/ssv-delly.config @@ -11,9 +11,9 @@ params { blcds_registered_dataset = false - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" - exclusion_file = "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" + exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" // select the tool(s) to run algorithm = ['delly'] diff --git a/test/config/ssv-manta.config b/test/config/ssv-manta.config index 0346f1b..ed71e32 100644 --- a/test/config/ssv-manta.config +++ b/test/config/ssv-manta.config @@ -11,9 +11,9 @@ params { blcds_registered_dataset = false - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" - exclusion_file = "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" + exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv" // select the tool(s) to run algorithm = ['manta'] diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 0b4ab6d..0292109 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -68,7 +68,7 @@ "docker_image_delly": "ghcr.io/uclahs-cds/delly:1.2.6", "docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0", "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", - "exclusion_file": "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv", + "exclusion_file": "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv", "filter_condition": "FILTER=\\='PASS'", "input": { "BAM": { @@ -138,7 +138,7 @@ "memory": "1 GB" } }, - "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", "sample": "610093", "sample_id": "TWGSAMIN000001", "samples_to_process": [