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Merge pull request #106 from broadinstitute/dp-classify
strip out blastx from classify_multi workflow
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| # Documentation | ||
| # https://cromwell.readthedocs.io/en/stable/backends/Local/ | ||
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| # Define a new backend provider. | ||
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| LocalExample { | ||
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| # The actor that runs the backend. In this case, it's the Shared File System (SFS) ConfigBackend. | ||
| actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory" | ||
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| # The backend custom configuration. | ||
| config { | ||
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| # Optional limits on the number of concurrent jobs | ||
| concurrent-job-limit = 1 | ||
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| # If true submits scripts to the bash background using "&". Only usefull for dispatchers that do NOT submit | ||
| # the job and then immediately return a scheduled job id. | ||
| run-in-background = true | ||
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| # `temporary-directory` creates the temporary directory for commands. | ||
| # | ||
| # If this value is not set explicitly, the default value creates a unique temporary directory, equivalent to: | ||
| # temporary-directory = "$(mktemp -d \"$PWD\"/tmp.XXXXXX)" | ||
| # | ||
| # The expression is run from the execution directory for the script. The expression must create the directory | ||
| # if it does not exist, and then return the full path to the directory. | ||
| # | ||
| # To create and return a non-random temporary directory, use something like: | ||
| # temporary-directory = "$(mkdir -p /tmp/mydir && echo /tmp/mydir)" | ||
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| # `script-epilogue` configures a shell command to run after the execution of every command block. | ||
| # | ||
| # If this value is not set explicitly, the default value is `sync`, equivalent to: | ||
| # script-epilogue = "sync" | ||
| # | ||
| # To turn off the default `sync` behavior set this value to an empty string: | ||
| # script-epilogue = "" | ||
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| # `glob-link-command` specifies command used to link glob outputs, by default using hard-links. | ||
| # If filesystem doesn't allow hard-links (e.g., beeGFS), change to soft-links as follows: | ||
| # glob-link-command = "ln -sL GLOB_PATTERN GLOB_DIRECTORY" | ||
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| # The list of possible runtime custom attributes. | ||
| runtime-attributes = """ | ||
| String? docker | ||
| String? docker_user | ||
| """ | ||
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| # Submit string when there is no "docker" runtime attribute. | ||
| submit = "/usr/bin/env bash ${script}" | ||
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| # Submit string when there is a "docker" runtime attribute. | ||
| submit-docker = """ | ||
| docker run \ | ||
| --rm -i \ | ||
| ${"--user " + docker_user} \ | ||
| --entrypoint ${job_shell} \ | ||
| -v ${cwd}:${docker_cwd} \ | ||
| ${docker} ${script} | ||
| """ | ||
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| # Root directory where Cromwell writes job results. This directory must be | ||
| # visible and writeable by the Cromwell process as well as the jobs that Cromwell | ||
| # launches. | ||
| root = "cromwell-executions" | ||
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| # Root directory where Cromwell writes job results in the container. This value | ||
| # can be used to specify where the execution folder is mounted in the container. | ||
| # it is used for the construction of the docker_cwd string in the submit-docker | ||
| # value above. | ||
| dockerRoot = "/cromwell-executions" | ||
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| # File system configuration. | ||
| filesystems { | ||
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| # For SFS backends, the "local" configuration specifies how files are handled. | ||
| local { | ||
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| # Try to hard link (ln), then soft-link (ln -s), and if both fail, then copy the files. | ||
| localization: [ | ||
| "hard-link", "soft-link", "copy" | ||
| ] | ||
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| # Call caching strategies | ||
| caching { | ||
| # When copying a cached result, what type of file duplication should occur. | ||
| # For more information check: https://cromwell.readthedocs.io/en/stable/backends/HPC/#shared-filesystem | ||
| duplication-strategy: [ | ||
| "hard-link", "soft-link", "copy" | ||
| ] | ||
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| # Strategy to determine if a file has been used before. | ||
| # For extended explanation and alternative strategies check: https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching | ||
| hashing-strategy: "md5" | ||
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| # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash. | ||
| # If false or the md5 does not exist, will proceed with the above-defined hashing strategy. | ||
| check-sibling-md5: false | ||
| } | ||
| } | ||
| } | ||
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| # The defaults for runtime attributes if not provided. | ||
| default-runtime-attributes { | ||
| failOnStderr: false | ||
| continueOnReturnCode: 0 | ||
| } | ||
| } | ||
| } |
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