upload run command now accepts "MiSeqi100" and "MiSeqi100Plus" instrument types.launch application where app session names were not set via form options -o app-session-name (or -o ICAPipelineParameter__app-session-name for ICA-based applications).
--appsession-label takes precedence, if set.--retry flag is deprecated (as it is effectively always supplied)upload run where in rare cases a file upload may fail but the upload command can still complete successfullyget file and content: fixed bug where file field names did not match API response (e.g. FilePath is now Path)launch application: fixed bug where launches with file inputs would sometimes fail with the error "failed translating file ID"launch application) could be timed out while waiting for a response. The timeout for all commands has been extended to 6 minutes.:) on Windowscontents commandupload run failed setting run name (also known as instrument ID) and flow cell barcode. Values for these fields are parsed from RunInfo.xml by default, but can be overridden using --run-id and --flowcell.list flattened JSON array outputs when there was a single result. Output JSON (when using -f json) will now consistently be an array for list commands.+), dollar ($) and ampersand (&)appsession logs: list log files for an appsession, exposing their IDs which can then (for example) be used with download file to retrieve the log contents# download all log files for a given appsession into the current working directory $ bs appsession logs 123456 --terse | xargs -n1 bs download file --no-metadata -i # download log files with a .log extension $ bs appsession logs 123456 --terse --extension log | xargs -n1 bs download file --no-metadata -i
appsession children: show the child appsessions for an analysis workflow or multi-node parent appsessiondataset copy: call the remote Sequence Hub copy function for FASTQ datasets, duplicating file data in a new projectlaunch application:
--no-defaults as an advanced option to prevent the CLI filling in default options for a launch--option-help to pull the tooltip text, if present, for a given launch option$ bs launch application -n 'DRAGEN Germline' --app-version 3.9.5 --option-help project-id +------------+-----------------------------------------------+ | Option | Help | +------------+-----------------------------------------------+ | project-id | Select a project to save analysis results to. | +------------+-----------------------------------------------+
download:
-o .)--summary)upload run:
--run-parameters) which may be located outside of the run folder being uploaded download: fixed regression introduced in v1.4.0 where files were queued before the download starts, delaying large downloads (such as runs) from starting while the file list was gatheredupload dataset:
= or + in their filenamelaunch application:
yield biosample returns the yields for all library prep kits for a given biosample:> bs yield biosample -i 123456 +--------------------+----------------+------------------+ | LibraryPrep.Name | LibraryPrep.Id | TotalActualYield | +--------------------+----------------+------------------+ | TruSight Tumor 170 | 1425425 | 10938006090 | +--------------------+----------------+------------------+
upload,download and contents: added --include and --exclude flags for flexible subsetting of file sets using UNIX-style wildcard patterns:> bs contents dataset -i ds.ad11a51e883f4f399a779dd86c8586ed --exclude '*' --include '*.vcf.*' --exclude '*.ploidy.*' +-------------+-----------------------------------------------+ | Id | FilePath | +-------------+-----------------------------------------------+ | 21100442038 | NA12878-PCRF450-1.cnv.vcf.gz | | 21100442039 | NA12878-PCRF450-1.cnv.vcf.gz.md5sum | | 21100442040 | NA12878-PCRF450-1.cnv.vcf.gz.tbi | | 21100442048 | NA12878-PCRF450-1.hard-filtered.vcf.gz | | 21100442049 | NA12878-PCRF450-1.hard-filtered.vcf.gz.md5sum | | 21100442050 | NA12878-PCRF450-1.hard-filtered.vcf.gz.tbi | | 21100442066 | NA12878-PCRF450-1.sv.vcf.gz | | 21100442067 | NA12878-PCRF450-1.sv.vcf.gz.tbi | +-------------+-----------------------------------------------+
upload run:
--quiet flag to suppress all feedback on transfer progress (both progress bars and file-by-file completion)--id flag list appsession:
--qc-status option to filter by QC status (e.g. bs list appsessions --qc-status QCFailed)--delivery-status option to filter by delivery status (e.g. bs list appsessions --delivery-status ReadyForDelivery)update project: added the ability to edit a project's description:
> bs update project --field-name description --field-content 'My new project description'
seqstats run: added additional metric fieldsINFO and DEBUG log messages (enabled using -vvvv) are now written to standard error (stderr) rather than standard outputupload: fix bug where temporary upload credentials may expire during very long uploads (more than 24 hours)upload run: fix bug where an upload may fail, and the run is marked Upload Failed, but the CLI exits with a success exit code (0)download appsession downloads all the output datasets of a given appsession (and appsession contents lists an appsession's output files)
$ bs download appsession -i 123456 -o my-appsession
update dataset allows changing the QC Status of a dataset
$ bs update dataset -i ds.1234567abcdef --field-name qc-status --field-content QcPassed
download: added --no-metadata flag to skip writing a metadata JSON fileupload: progress bars are now automatically turned off when uploading more than 1,000 files (common when uploading runs). This avoids issues seen with drawing huge numbers of progress bars. A lightweight file-by-file progress summary is shown instead.contents: Added --filter-field and --filter-term enabling more flexible filtering using regex, for example: bs contents appsession -i 123456 --filter-field FilePath --filter-term 'NA1287[78]'-vvvvvv logging option which is currently only used to output additional part-by-part granular upload request information to help debuggingupload dataset: added --appsession flag which returns (only) the appsession used to upload data. This enables an 'upload data then launch an app' pattern, e.g. by chaining await appsession on the output of upload dataset --appsessionhistory: add --page-size argument to enable user optimisation when retrieving many history recordsupload: fixed bug where empty 0 byte files were not uploadedupload run: fixed bug where user cancelling (e.g. Ctrl+C) would sometimes not mark the run as Upload FailedTweaks to existing commands:
auth: now requests the CREATE RUNS scope by defaultBugs fixed:
upload run: SequenceComplete.txt) will now be uploaded rather than skipped--skip-dir arguments with a trailing path separator was ignoredrunParameters.xml as well as RunParameters.xml across all supported OSNew commands:
upload run: simple, fast and robust upload of a local run folder to Sequence Hub!accession manifest: upload a biosample manifest from the command line to create biosamples, attach metadata and queue analysis workflowsupdate biosample / appsession: use this to edit a biosample default project or change an appsession’s execution status, for examplerevoke config: expire an access token and delete the CLI configuration fileseqstats run: get statistics for a run such as Yield and % PFTweaks to existing commands:
upload: fine-grained concurrency controls added (--concurrent-files and --concurrent-parts)upload dataset: clearer error reporting when no files found to uploadBugs fixed:
upload dataset: FASTQ filenames with sample numbers >999 now accepted as validupload: fixed bug where file handles weren’t closed as upload completesdownload: --no-progress-bars no longer shows one progress bartrash management commands: list, empty and restorehistory for accessing enterprise account audit logsrename run for the new run rename feature added in BSSH v5.40list datasets: add --input-run filter flaglist datasets/appsessions: add --input-biosample-id filter flagget appsession: add compute statistics fields to outputload config: if no config passed, use defaultdelete project: fix bug where deleting a shared project gave an EOF errorupload dataset: fix bug in fastq upload with --recursive where directory structure was retainedlist datasets: fix bug where filtering by both project and type caused type to be ignored--app-version--recursive flagunlock biosample enables auto-aggregated biosamples to be used in app launcheslink file returns a signed S3 link for a given file ID--project-name, --project-id and --input-run--appresults)--appsession-label argument to rename upload appsession--stdout / --stderr to avoid collisions with other flagsbs await appsessionbs upload dataset:
--type common.filesbs translate appresult and bs translate datasetbs await appsessionbs download: add ability to download uncompressedbs application launch: Add support for TabularFieldset bs create project:
bs list biosample: add --projectid switchbs create workflow: Slightly improve usability