PacificBiosciences · williamrowell · Jan 10, 2025 · Dec 9, 2024 · Dec 9, 2024 · Dec 9, 2024
diff --git a/README.md b/README.md
@@ -24,25 +24,25 @@ Both workflows are designed to analyze human PacBio whole genome sequencing (WGS
 
 This is an actively developed workflow with multiple versioned releases, and we make use of git submodules for common tasks that are shared by multiple workflows. There are two ways to ensure you are using a supported release of the workflow and ensure that the submodules are correctly initialized:
 
-1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.0.7):
+1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.1.0):
 
   ```bash
-  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-singleton.zip
-  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-family.zip
+  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.0/hifi-human-wgs-singleton.zip
+  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.0/hifi-human-wgs-family.zip
   ```
 
 2) Clone the repository and initialize the submodules:
 
   ```bash
   git clone \
-    --depth 1 --branch v2.0.7 \
+    --depth 1 --branch v2.1.0 \
     --recursive \
     https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git
   ```
 
 ## Resource requirements
 
-The most resource-heavy step in the workflow requires 64 cores and 256 GB of RAM. Ensure that the backend environment you're using has enough quota to run the workflow.
+The most resource-heavy step in the workflow requires 64 cpu cores and 256 GB of RAM. Ensure that the backend environment you're using has enough quota to run the workflow.
 
 On some backends, you may be able to make use of a GPU to accelerate the DeepVariant step.  The GPU is not required, but it can significantly speed up the workflow.  If you have access to a GPU, you can set the `gpu` parameter to `true` in the inputs JSON file.
 

diff --git a/docs/backend-hpc.md b/docs/backend-hpc.md
@@ -13,6 +13,14 @@ Either `miniwdl` or `Cromwell` can be used to run workflows on the HPC.
 
 An [example miniwdl.cfg file](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/main/backends/hpc/miniwdl.cfg) is provided here. This should be placed at `~/.config/miniwdl.cfg` and edited to match your slurm configuration. This allows running workflows using a basic SLURM setup.
 
+> [!IMPORTANT]
+> In order to simplify workflow inputs, we make use of `map` files to specify the input data. This allows for a more concise input file, but requires changing a miniwdl configuration option to allow workflows to access files that are not expressly supplied with workflow inputs.  To enable this, add the following line to your `miniwdl.cfg` file:
+> ```ini
+> [file_io]
+> allow_any_input = true
+> ```
+> This option is already included in the example miniwdl.cfg file described in this section.
+
 ## Installing and configuring `Cromwell`
 
 Cromwell supports a number of different HPC backends; see [Cromwell's documentation](https://cromwell.readthedocs.io/en/stable/backends/HPC/) for more information on configuring each of the backends.  Cromwell can be used in a standalone "run" mode, or in "server" mode to allow for multiple users to submit workflows.  In the example below, we provide example commands for running Cromwell in "run" mode.

diff --git a/docs/family.md b/docs/family.md
@@ -119,7 +119,7 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | File | stats_file | Table of summary statistics |  |
 | Array\[File\] | bam_stats | BAM stats | Per-read length and read-quality |
 | Array\[File\] | read_length_plot | Read length plot |  |
-| Array\[File\] | read_quality_plot | Read quality plot |  |
+| Array\[File?\] | read_quality_plot | Read quality plot |  |
 | Array\[File\] | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
 | Array\[File\] | merged_haplotagged_bam_index |  |  |
 | Array\[File\] | mosdepth_summary | Summary of aligned read depth. |  |
@@ -223,15 +223,15 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
-| Array\[File\] | cpg_hap1_bed | CpG hap1 BED |  |
-| Array\[File\] | cpg_hap1_bed_index |  |  |
-| Array\[File\] | cpg_hap2_bed | CpG hap2 BED |  |
-| Array\[File\] | cpg_hap2_bed_index |  |  |
-| Array\[File\] | cpg_combined_bed | CpG combined BED |  |
-| Array\[File\] | cpg_combined_bed_index |  |  |
-| Array\[File\] | cpg_hap1_bw | CpG hap1 BigWig |  |
-| Array\[File\] | cpg_hap2_bw | CpG hap2 BigWig |  |
-| Array\[File\] | cpg_combined_bw | CpG combined BigWig |  |
+| Array\[File?\] | cpg_hap1_bed | CpG hap1 BED |  |
+| Array\[File?\] | cpg_hap1_bed_index |  |  |
+| Array\[File?\] | cpg_hap2_bed | CpG hap2 BED |  |
+| Array\[File?\] | cpg_hap2_bed_index |  |  |
+| Array\[File?\] | cpg_combined_bed | CpG combined BED |  |
+| Array\[File?\] | cpg_combined_bed_index |  |  |
+| Array\[File?\] | cpg_hap1_bw | CpG hap1 BigWig |  |
+| Array\[File?\] | cpg_hap2_bw | CpG hap2 BigWig |  |
+| Array\[File?\] | cpg_combined_bw | CpG combined BigWig |  |
 | Array\[String\] | stat_cpg_hap1_count | Hap1 CpG count |  |
 | Array\[String\] | stat_cpg_hap2_count | Hap2 CpG count |  |
 | Array\[String\] | stat_cpg_combined_count | Combined CpG count |  |
@@ -241,10 +241,10 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
 | Array\[File\] | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci |
-| Array\[File\] | pharmcat_match_json | PharmCAT match JSON |  |
-| Array\[File\] | pharmcat_phenotype_json | PharmCAT phenotype JSON |  |
-| Array\[File\] | pharmcat_report_html | PharmCAT report HTML |  |
-| Array\[File\] | pharmcat_report_json | PharmCAT report JSON |  |
+| Array\[File?\] | pharmcat_match_json | PharmCAT match JSON |  |
+| Array\[File?\] | pharmcat_phenotype_json | PharmCAT phenotype JSON |  |
+| Array\[File?\] | pharmcat_report_html | PharmCAT report HTML |  |
+| Array\[File?\] | pharmcat_report_json | PharmCAT report JSON |  |
 
 ### Tertiary Analysis
 

diff --git a/docs/pharmcat.md b/docs/pharmcat.md
@@ -8,3 +8,7 @@ flowchart TD
   filter --> pharmcat["PharmCat"]
   pharmcat --> outputs[/"PharmCat outputs"/]
 ```
+
+[PharmCat (Pharmacogenomics Clinical Annotation Tool)](https://pharmcat.org) analyzes genetic variants and predicts drug response.  In this subworkflow implementation, PharmCat will use a combination of the small variant VCF and pbStarPhase outupts.  PharmCat outputs will only be generated if the depth at the variant position is greater than `pharmcat_min_coverage` (default `10`).  If no variants pass this filter, no outputs will be generated.
+
+Citation: K Sangkuhl & M Whirl-Carrillo, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2020) 107(1):203-210. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977333](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977333).
diff --git a/docs/singleton.md b/docs/singleton.md
@@ -84,7 +84,7 @@ flowchart TD
 | File | stats_file | Table of summary statistics |  |
 | File | bam_stats | BAM stats | Per-read length and read-quality |
 | File | read_length_plot | Read length plot |  |
-| File | read_quality_plot | Read quality plot |  |
+| File? | read_quality_plot | Read quality plot |  |
 | File | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
 | File | merged_haplotagged_bam_index |  |  |
 | File | mosdepth_summary | Summary of aligned read depth. |  |
@@ -182,15 +182,15 @@ flowchart TD
 
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
-| File | cpg_hap1_bed | CpG hap1 BED |  |
-| File | cpg_hap1_bed_index |  |  |
-| File | cpg_hap2_bed | CpG hap2 BED |  |
-| File | cpg_hap2_bed_index |  |  |
-| File | cpg_combined_bed | CpG combined BED |  |
-| File | cpg_combined_bed_index |  |  |
-| File | cpg_hap1_bw | CpG hap1 BigWig |  |
-| File | cpg_hap2_bw | CpG hap2 BigWig |  |
-| File | cpg_combined_bw | CpG combined BigWig |  |
+| File? | cpg_hap1_bed | CpG hap1 BED |  |
+| File? | cpg_hap1_bed_index |  |  |
+| File? | cpg_hap2_bed | CpG hap2 BED |  |
+| File? | cpg_hap2_bed_index |  |  |
+| File? | cpg_combined_bed | CpG combined BED |  |
+| File? | cpg_combined_bed_index |  |  |
+| File? | cpg_hap1_bw | CpG hap1 BigWig |  |
+| File? | cpg_hap2_bw | CpG hap2 BigWig |  |
+| File? | cpg_combined_bw | CpG combined BigWig |  |
 | String | stat_cpg_hap1_count | Hap1 CpG count |  |
 | String | stat_cpg_hap2_count | Hap2 CpG count |  |
 | String | stat_cpg_combined_count | Combined CpG count |  |
@@ -200,10 +200,10 @@ flowchart TD
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
 | File | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci |
-| File | pharmcat_match_json | PharmCAT match JSON |  |
-| File | pharmcat_phenotype_json | PharmCAT phenotype JSON |  |
-| File | pharmcat_report_html | PharmCAT report HTML |  |
-| File | pharmcat_report_json | PharmCAT report JSON |  |
+| File? | pharmcat_match_json | PharmCAT match JSON |  |
+| File? | pharmcat_phenotype_json | PharmCAT phenotype JSON |  |
+| File? | pharmcat_report_html | PharmCAT report HTML |  |
+| File? | pharmcat_report_json | PharmCAT report JSON |  |
 
 ### Tertiary Analysis