From 7be71512a73f724db111d15e2ac8ebf0ee5713c4 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 20 Feb 2024 12:52:42 -0800 Subject: [PATCH 1/3] Updated license year. --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index aaea0c14..9d176165 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright (c) 2023, Pacific Biosciences of California, Inc. +Copyright (c) 2024, Pacific Biosciences of California, Inc. All rights reserved. From eb3bbeb224dddb5d2fa3575fd93171e4f94e7197 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 20 Feb 2024 12:57:22 -0800 Subject: [PATCH 2/3] docs: Described restrictions on sample_id and cohort_id. --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index b2d3e201..c076bb09 100644 --- a/README.md +++ b/README.md @@ -115,7 +115,7 @@ A cohort can include one or more samples. Samples need not be related, but if yo | Type | Name | Description | Notes | | :- | :- | :- | :- | -| String | cohort_id | A unique name for the cohort; used to name outputs | | +| String | cohort_id | A unique name for the cohort; used to name outputs | Alphanumeric characters, underscore (`_`), and dash (`-`) are allowed. | | Array[[Sample](#sample)] | samples | The set of samples for the cohort. At least one sample must be defined. | | | Array[String] | phenotypes | [Human Phenotype Ontology (HPO) phenotypes](https://hpo.jax.org/app/) associated with the cohort. If no particular phenotypes are desired, the root HPO term, `"HP:0000001"`, can be used. | | @@ -125,12 +125,12 @@ Sample information for each sample in the workflow run. | Type | Name | Description | Notes | | :- | :- | :- | :- | -| String | sample_id | A unique name for the sample; used to name outputs | | +| String | sample_id | A unique name for the sample; used to name outputs | Alphanumeric characters, underscore (`_`), and dash (`-`) are allowed. | | Array[[IndexData](https://github.com/PacificBiosciences/wdl-common/blob/main/wdl/structs.wdl)] | movie_bams | The set of unaligned movie BAMs associated with this sample | | | String? | sex | Sample sex | ["MALE", "FEMALE", `null`]. If the sex field is missing or `null`, sex will be set to unknown. Used to set the expected sex chromosome karyotype for TRGT and HiFiCNV. | | Boolean | affected | Is this sample affected by the phenotype? | \[`true`, `false`\] | -| String? | father_id | Paternal `sample_id` | | -| String? | mother_id | Maternal `sample_id` | | +| String? | father_id | Paternal `sample_id` | Alphanumeric characters, underscore (`_`), and dash (`-`) are allowed. | +| String? | mother_id | Maternal `sample_id` | Alphanumeric characters, underscore (`_`), and dash (`-`) are allowed. | ## [ReferenceData](workflows/humanwgs_structs.wdl) From c463d01ed6d3dc30bc107f8cf08cd6cb6c03ca1e Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 20 Feb 2024 12:58:43 -0800 Subject: [PATCH 3/3] docs: Noted that only DeepVariant 1.6 is supported. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c076bb09..3dc28bb3 100644 --- a/README.md +++ b/README.md @@ -172,7 +172,7 @@ These files are hosted publicly in each of the cloud backends; see `backends/${b | Type | Name | Description | Notes | | :- | :- | :- | :- | -| String? | deepvariant_version | Version of deepvariant to use \["1.6.0"\] | | +| String? | deepvariant_version | Version of deepvariant to use \["1.6.0"\] | This release is only compatible with DeepVariant [1.6](https://github.com/google/deepvariant/releases/tag/v1.6.0). | | File? | custom_deepvariant_model_tar | Optional alternate DeepVariant [custom model](https://github.com/PacificBiosciences/wdl-common/blob/8d868818b62345fdb64ab104238d406d65334b3e/wdl/workflows/deepvariant/README.md) to use | | | Int? | pbsv_call_mem_gb | Optionally set RAM (GB) for pbsv_call during cohort analysis | | | Int? | glnexus_mem_gb | Optionally set RAM (GB) for GLnexus during cohort analysis | |