Release v5.0.0-rc.1 (#107)

* Update metadata.yaml

* Update README.md

* Update CHANGELOG.md

* Add contributors section

* update pipeline version in nextflow.config

* update README

* Update Release date in CHANGELOG.md

---------

Co-authored-by: Mootor <mmootor@ip-0A125217.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to the call-gSV pipeline.
 ---
 
 ## [Unreleased]
+
+---
+
+## [5.0.0-rc.1] - 2023-10-30
 ### Changed
 - Standardize DELLY output filenames
 - Enable `save_intermediate_files` in `bcftools.nf` and `rtgtools.nf`

README.md

@@ -63,7 +63,7 @@ Pipelines should be run **WITH A SINGLE SAMPLE AT TIME**. Otherwise resource all
 nextflow run path/to/main.nf -config path/to/sample-specific.config
 ```
 
-* For example, `path/to/main.nf` could be: `/hot/software/pipeline/pipeline-call-gSV/Nextflow/release/4.0.0/main.nf`
+* For example, `path/to/main.nf` could be: `/hot/software/pipeline/pipeline-call-gSV/Nextflow/release/5.0.0-rc.1/main.nf`
 * `path/to/sample-specific.config` is the path to where you saved your project-specific copy of [template.config](config/template.config)
 * `path/to/input.yaml` is the path to where you saved your sample-specific copy of [call-gSV-input.yaml](input/call-gSV-input.yaml)
 
@@ -184,16 +184,17 @@ 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`. |
+| `variant_type` | yes | list | List containing variant types to call. Default is `["gSV", "gCNV"]` |
 | `run_discovery` | yes | boolean | Specifies whether or not to run the "disovery" branch of the pipeline. Default value is `true`. (either `run_discovery` or `run_regenotyping` must be `true`) |
 | `run_regenotyping` | yes | boolean | Specifies whether or not to run the "regenotyping" branch of the pipeline. Default value is `false`. (either `run_discovery` or `run_regenotyping` must be `true`) |
 | `merged_sites` | yes | path | The path to the merged sites.bcf file. Must be populated if running the regenotyping branch. |
-| `reference_fasta` | yes | path | Absolute path to the reference genome `FASTA` file. The reference genome is used by Delly for SV calling. |
-| `exclusion_file` | yes | path | Absolute path to the delly reference genome `exclusion` file utilized to remove suggested regions for SV calling. On Slurm, an HG38 exclusion file is located at `/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv` |
-| `mappability_map` | yes | path | Absolute path to the delly mappability map to support GC and mappability fragment correction in CNV calling |
-| `map_qual` | no | path | minimum paired-end (PE) mapping quaility threshold for Delly). |
 | `run_delly` | true | boolean | Whether or not the workflow should run Delly (either run_delly or run_manta must be set to `true`) |
 | `run_manta` | true | boolean | Whether or not the workflow should run Manta (either run_delly or run_manta must be set to `true`) |
 | `run_qc` | no | boolean | Optional parameter to indicate whether subsequent quality checks should be run on Delly outputs. Default value is `false`. |
+| `reference_fasta` | yes | path | Absolute path to the reference genome `FASTA` file. The reference genome is used by Delly for SV calling. |
+| `exclusion_file` | yes | path | Absolute path to the delly reference genome `exclusion` file utilized to remove suggested regions for SV calling. On Slurm, an HG38 exclusion file is located at `/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv` |
+| `mappability_map` | yes | path | Absolute path to the delly mappability map to support GC and mappability fragment correction in CNV calling |
+| `map_qual` | no | path | minimum paired-end (PE) mapping quaility threshold for Delly. |
 | `save_intermediate_files` | yes | boolean | Optional parameter to indicate whether intermediate files will be saved. Default value is `false`. |
 | `output_dir` | yes | path | Absolute path to the directory where the output files to be saved. |
 | `work_dir` | optional | path | Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With `ucla_cds`, the default is `/scratch` and should only be changed for testing/development. Changing this directory to `/hot` or `/tmp` can lead to high server latency and potential disk space limitations, respectively. |
@@ -300,9 +301,10 @@ Included is a template for validating your input files. For more information on
 5. [Boutros Lab -CallSV Quality Control pipeline]()
 6. [The 1000 Genomes Project Consortium., Corresponding authors., Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015). https://doi.org/10.1038/nature15393](https://www.nature.com/articles/nature15393)
 
-## License
+## Contributors
+Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-call-gSV/graphs/contributors) at GitHub.
 
-Authors: Tim Sanders ([email protected]), Yu Pan ([email protected]), Yael Berkovich ([email protected]), Mohammed Faizal Eeman Mootor ([email protected])
+## License
 
 The pipeline-call-gSV is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 

metadata.yaml

@@ -5,4 +5,4 @@ maintainers: "Boutros Lab Infrastructure [email protected]
 languages: ["Nextflow", "Docker"]
 dependencies: ["Java", "Nextflow", "Docker"]
 references: "https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189620/Guide+to+Nextflow"
-tools: ["Delly:v1.1.3", "Manta:v1.6.0", "BCFtools:v1.15.1", "VCFtools:v0.1.16", "RTG-tools:v3.12", "PipeVal:v3.0.0"]
+tools: ["Delly:v1.1.3", "Manta:v1.6.0", "BCFtools:v1.15.1", "VCFtools:v0.1.16", "RTG-tools:v3.12", "PipeVal:v4.0.0-rc.2"]

nextflow.config

@@ -4,5 +4,5 @@ manifest {
     name = 'call-gSV'
     author = 'Yu Pan, Tim Sanders, Yael Berkovich, Mohammed Faizal Eeman Mootor'
     description = 'A pipeline to call germline structural variants utilizing Delly and Manta'
-    version = '4.0.1'
+    version = '5.0.0-rc.1'
 }