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Merge remote-tracking branch 'origin/master' into add-homebrew
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‎.github/workflows/build.yml‎

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- name: Setup Graalvm
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uses: graalvm/setup-graalvm@v1
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with:
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java-version: '17.0.8'
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java-version: '21'
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distribution: 'graalvm'
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components: 'native-image'
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native-image-musl: 'true'
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mac-image:
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name: MAC
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runs-on: macos-latest
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runs-on: macos-latest-large
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timeout-minutes: 90
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steps:
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- name: Setup Graalvm
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uses: graalvm/setup-graalvm@v1
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with:
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java-version: '17.0.8'
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java-version: '21'
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distribution: 'graalvm'
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components: 'native-image'
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github-token: ${{ secrets.GITHUB_TOKEN }}
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uses: graalvm/setup-graalvm@v1
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with:
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version: 'latest'
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java-version: '17.0.8'
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java-version: '21'
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distribution: 'graalvm'
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components: 'native-image'
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github-token: ${{ secrets.GITHUB_TOKEN }}
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- name: Setup Graalvm
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uses: graalvm/setup-graalvm@v1
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with:
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java-version: '17.0.8'
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java-version: '21'
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distribution: 'graalvm'
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components: 'native-image'
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github-token: ${{ secrets.GITHUB_TOKEN }}
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- name: Setup Java for JReleaser
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uses: actions/setup-java@v4
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with:
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java-version: 17.0.8
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java-version: '21'
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distribution: 'adopt'
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- name: Version

‎.gitignore‎

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# Ignore Gradle project-specific cache directory
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.gradle
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.idea
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.env
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# Ignore Gradle build output directory
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build
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**/build-info.properties
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# Location for unshared files
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.user/
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.user/
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*.iml

‎.sdkmanrc‎

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# Enable auto-env through the sdkman_auto_env config
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# Add key=value pairs of SDKs to use below
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java=17.0.8-graalce
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java=21.0.4-graal

‎README.md‎

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@@ -175,4 +175,4 @@ Run a non-binary development version by executing the [`./tw`](tw) script in the
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## License
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[Mozilla Public License v2.0](https://github.com/seqeralabs/tower-cli/blob/master/LICENSE.txt)
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[Apache 2.0](https://github.com/seqeralabs/tower-cli/blob/master/LICENSE.txt)

‎USAGE.md‎

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Workflow 1XCXxX0vCX8xhx submitted at user workspace.
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https://tower.nf/user/abhinav/watch/1XCXxX0vCX8xhx
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https://cloud.seqera.io/user/abhinav/watch/1XCXxX0vCX8xhx
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```
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When using `--wait`, `tw` can exit with one of two exit codes:
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Workflow 2XDXxX0vCX8xhx submitted at user workspace.
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https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx
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https://cloud.seqera.io/user/abhinav/watch/2XDXxX0vCX8xhx
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```
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See [Nextflow configuration][nextflow-config] for more information.
@@ -236,7 +236,7 @@ $ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_para
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Workflow 2XDXxX0vCX8xhx submitted at user workspace.
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https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx
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https://cloud.seqera.io/user/abhinav/watch/2XDXxX0vCX8xhx
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```
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- Pipeline parameters are defined within the `custom_rnaseq_params.yaml` file.
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Run `tw workspaces -h` to view supported workspace operations.
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Run `tw workspaces add -h` to view the required and optional fields for adding your workspace.
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Workspaces provide the context in which a user launches workflow executions, defines the available resources, and manages who can access those resources. Workspaces contain pipelines, runs, actions, datasets, compute environments, credentials, and secrets. Access permissions are controlled with participants, collaborators, and teams.
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Workspaces provide the context in which a user launches workflow executions, defines the available resources, and manages who can access those resources. Workspaces contain pipelines, runs, actions, compute environments, credentials, datasets, data links, and secrets. Access permissions are controlled with participants, collaborators, and teams.
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See [User workspaces][user-workspaces] for more information.
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Participant '[email protected]' has now role 'maintain' for workspace 'shared-workspace'
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```
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## Data Links
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Run `tw data-links -h` to view supported data link operations.
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Data links allow you to work with public and private cloud storage buckets in Data Explorer in the specified workspace. See [Data Explorer][data-explorer] for more information. AWS S3, Azure Blob Storage, and Google Cloud Storage are supported. The full list of operations are:
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- `list`: List data links in a workspace
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- `add`: Add a custom data link to a workspace
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- `update`: Update a custom data link in a workspace
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- `delete`: Delete a custom data link from a workspace
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- `browse`: Browse the contents of a data link in a workspace
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### List data links
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Run `tw data-links list -h` to view all the optional fields for listing data links in a workspace. If a workspace is not defined, the `TOWER_WORKSPACE_ID` workspace is used by default. Data links can be one of two types:
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- `v1-cloud-<id>`: **cloud** data links auto-discovered using credentials attached to the workspace
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- `v1-user-<id>`: **custom** data links created by users
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```console
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$ tw data-links list -w seqeralabs/showcase
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Data links at [seqeralabs / showcase] workspace:
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ID | Provider | Name | Resource ref | Region
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-------------------------------------------+----------+--------------------------------+-----------------------------------------------------------------+-----------
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v1-cloud-833bb845bd9ec1970c4a7b0bb7b8c4ad | aws | e2e-data-explorer-tests-aws | s3://e2e-data-explorer-tests-aws | eu-west-2
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v1-cloud-60700a33ec3fae68d424cf948fa8d10c | aws | nf-tower-bucket | s3://nf-tower-bucket | eu-west-1
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v1-user-09705781697816b62f9454bc4b9434b4 | aws | vscode-analysis-demo | s3://seqera-development-permanent-bucket/studios-demo/vscode/ | eu-west-2
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v1-user-0dede00fabbc4b9e2610261822a2d6ae | aws | seqeralabs-showcase | s3://seqeralabs-showcase | eu-west-1
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v1-user-171aa8801cabe4af71500335f193d649 | aws | projectA-rnaseq-analysis | s3://seqeralabs-showcase/demo/nf-core-rnaseq/ | eu-west-1
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<snip>
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v1-user-bb4fa9625a44721510c47ac1cb97905b | aws | genome-in-a-bottle | s3://giab | us-east-1
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v1-user-e7bf26921ba74032bd6ae1870df381fc | aws | NCBI_Sequence_Read_Archive_SRA | s3://sra-pub-src-1/ | us-east-1
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Showing from 0 to 99 from a total of 16 entries.
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```
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### Add a custom data link
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Run `tw data-links add -h` to view all the required and optional fields for adding a custom data link to a workspace. Users with the `MAINTAIN` role and above for a workspace can add custom data links. The data link `name`, `uri` and `provider` (one of `aws`, `azure`, or `google`) fields are required. If adding a custom data link for a private bucket, the `credentials` identifier field is also required. Adding a custom data link for a public bucket doesn't require credentials.
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```console
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$ tw data-links add -w seqeralabs/showcase -n FOO -u az://seqeralabs.azure-benchmarking -p azure -c seqera_azure_credentials
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Data link created:
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ID | Provider | Name | Resource ref | Region
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------------------------------------------+----------+------+------------------------------------+--------
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v1-user-152116183ee325463901430bb9efb8c9 | azure | FOO | az://seqeralabs.azure-benchmarking |
539+
```
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### Update a custom data link
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Run `tw data-links update -h` to view all the required and optional fields for updating a custom data link in a workspace. Users with the `MAINTAIN` role and above for a workspace can update custom data links.
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```console
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$ tw data-links update -w seqeralabs/showcase -i v1-user-152116183ee325463901430bb9efb8c9 -n BAR
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Data link updated:
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ID | Provider | Name | Resource ref | Region
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------------------------------------------+----------+------+------------------------------------+--------
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v1-user-152116183ee325463901430bb9efb8c9 | azure | BAR | az://seqeralabs.azure-benchmarking |
553+
```
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### Delete a custom data link
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Run `tw data-links delete -h` to view all the required and optional fields for deleting a custom data link from a workspace. Users with the `MAINTAIN` role and above for a workspace can delete custom data links.
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```console
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$ tw data-links delete -w seqeralabs/showcase -i v1-user-152116183ee325463901430bb9efb8c9
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Data link 'v1-user-152116183ee325463901430bb9efb8c9' deleted at '138659136604200' workspace.
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```
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### Browse the contents of a data link
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Run `tw data-links browse -h` to view all the required and optional fields for browsing a data link in a workspace. Define the data link id using the required `-i` or `--id` argument, which can be found by first using the `list` operation for a workspace. In the example below, a `name` is optionally defined to only retrieve data links with names that start with the given word:
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```console
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$ tw data-links list -w seqeralabs/showcase -n 1000genomes
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Data links at [seqeralabs / showcase] workspace:
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ID | Provider | Name | Resource ref | Region
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------------------------------------------+----------+-------------+------------------+-----------
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v1-user-6d8f44c239e2a098b3e02e918612452a | aws | 1000genomes | s3://1000genomes | us-east-1
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Showing from 0 to 99 from a total of 1 entries.
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$ tw data-links browse -w seqeralabs/showcase -i v1-user-6d8f44c239e2a098b3e02e918612452a
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Content of 's3://1000genomes' and path 'null':
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Type | Name | Size
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--------+--------------------------------------------+----------
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FILE | 20131219.populations.tsv | 1663
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FILE | 20131219.superpopulations.tsv | 97
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FILE | CHANGELOG | 257098
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FILE | README.alignment_data | 15977
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FILE | README.analysis_history | 5289
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FILE | README.complete_genomics_data | 5967
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FILE | README.crams | 563
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FILE | README.ebi_aspera_info | 935
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FILE | README.ftp_structure | 8408
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FILE | README.pilot_data | 2082
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FILE | README.populations | 1938
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FILE | README.sequence_data | 7857
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FILE | README_missing_files_20150612 | 672
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FILE | README_phase3_alignments_sequence_20150526 | 136
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FILE | README_phase3_data_move_20150612 | 273
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FILE | alignment.index | 3579471
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FILE | analysis.sequence.index | 54743580
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FILE | exome.alignment.index | 3549051
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FILE | sequence.index | 67069489
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FOLDER | 1000G_2504_high_coverage/ | 0
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FOLDER | alignment_indices/ | 0
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FOLDER | changelog_details/ | 0
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FOLDER | complete_genomics_indices/ | 0
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FOLDER | data/ | 0
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FOLDER | hgsv_sv_discovery/ | 0
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FOLDER | phase1/ | 0
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FOLDER | phase3/ | 0
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FOLDER | pilot_data/ | 0
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FOLDER | release/ | 0
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FOLDER | sequence_indices/ | 0
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FOLDER | technical/ | 0
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```
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[compute-envs]: https://docs.seqera.io/platform/latest/compute-envs/overview
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[credentials]: https://docs.seqera.io/platform/latest/credentials/overview
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[git-integration]: https://docs.seqera.io/platform/latest/git/overview
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[tower-agent]: https://github.com/seqeralabs/tower-agent
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[user-workspaces]: https://docs.seqera.io/platform/latest/orgs-and-teams/workspace-management
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[wave-docs]: https://www.nextflow.io/docs/latest/wave.html
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[data-explorer]: https://docs.seqera.io/platform/latest/data/data-explorer

‎VERSION‎

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0.9.2
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0.10.3

‎build.gradle‎

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id 'application'
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id 'jacoco'
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id 'org.cadixdev.licenser' version '0.6.1'
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id 'org.graalvm.buildtools.native'
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id 'org.graalvm.buildtools.native' version '0.10.2'
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id 'com.github.johnrengelman.shadow' version '7.1.2'
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}
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// define these in the `gradle.properties` file
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ext.githubUser = project.findProperty('github.packages.user')
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ext.githubToken = project.findProperty('github.packages.token')
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repositories {
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mavenCentral()
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maven {
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credentials {
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username = System.getenv("GITHUB_USERNAME")
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password = System.getenv("GITHUB_TOKEN")
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username = githubUser ?: System.getenv("GITHUB_USERNAME")
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password = githubToken ?: System.getenv("GITHUB_TOKEN")
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}
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}
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}
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implementation 'io.seqera.tower:tower-java-sdk:1.9.5'
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implementation 'io.seqera.tower:tower-java-sdk:1.9.9'
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implementation 'info.picocli:picocli:4.6.3'
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java {
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toolchain {
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languageVersion = JavaLanguageVersion.of(21)
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}
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}
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compileJava {
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targetCompatibility = JavaVersion.toVersion("11")
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graalvmNative {
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toolchainDetection = true
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binaries {
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javaLauncher = javaToolchains.launcherFor {
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languageVersion = JavaLanguageVersion.of(21)
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vendor = JvmVendorSpec.matching("Oracle Corporation")
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}
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test {
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verbose = true
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agent = false
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}
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}
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}

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