1.4.0 (2021-06-23)

New commands

  • 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      |
+--------------------+----------------+------------------+

Tweaks to existing commands

  • 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:
    • Added --quiet flag to suppress all feedback on transfer progress (both progress bars and file-by-file completion)
    • Returns uploaded run metadata on completion
    • Removed --id flag
  • list appsession:
    • added --qc-status option to filter by QC status (e.g. bs list appsessions --qc-status QCFailed)
    • added --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 fields

Bugs fixed

  • INFO and DEBUG log messages (enabled using -vvvv) are now written to standard error (stderr) rather than standard output

1.3.1 (2021-03-22)

Bugs fixed

  • upload: 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)

1.3.0 (2021-02-16)

New commands

  • 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

Tweaks to existing commands

  • download: added --no-metadata flag to skip writing a metadata JSON file
  • upload: 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]'
  • All commands: added an even more verbose -vvvvvv logging option which is currently only used to output additional part-by-part granular upload request information to help debugging
  • upload 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 --appsession
  • history: add --page-size argument to enable user optimisation when retrieving many history records

Bugs fixed

  • upload: fixed bug where empty 0 byte files were not uploaded
  • upload run: fixed bug where user cancelling (e.g. Ctrl+C) would sometimes not mark the run as Upload Failed

1.2.1 (2020-08-12)

  • Tweaks to existing commands:

    • auth: now requests the CREATE RUNS scope by default
  • Bugs fixed:

    • upload run:
    • any empty files (e.g. SequenceComplete.txt) will now be uploaded rather than skipped
    • fixed a bug where --skip-dir arguments with a trailing path separator was ignored
    • now accepts runParameters.xml as well as RunParameters.xml across all supported OS

1.2.0 (2020-05-29)

  • New 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 workflows
    • update biosample / appsession: use this to edit a biosample default project or change an appsession’s execution status, for example
    • revoke config: expire an access token and delete the CLI configuration file
    • seqstats run: get statistics for a run such as Yield and % PF
  • Tweaks to existing commands:

    • upload: fine-grained concurrency controls added (--concurrent-files and --concurrent-parts)
    • upload dataset: clearer error reporting when no files found to upload
  • Bugs fixed:

    • upload dataset: FASTQ filenames with sample numbers >999 now accepted as valid
    • upload: fixed bug where file handles weren’t closed as upload completes
    • download: --no-progress-bars no longer shows one progress bar

1.1.0 (2019-12-05)

  • New commands:
    • trash management commands: list, empty and restore
    • history for accessing enterprise account audit logs
    • rename run for the new run rename feature added in BSSH v5.40
  • Tweaks to existing commands:
    • list datasets: add --input-run filter flag
    • list datasets/appsessions: add --input-biosample-id filter flag
    • get appsession: add compute statistics fields to output
    • load config: if no config passed, use default
  • Bugs fixed:
    • delete project: fix bug where deleting a shared project gave an EOF error
    • upload dataset: fix bug in fastq upload with --recursive where directory structure was retained
    • list datasets: fix bug where filtering by both project and type caused type to be ignored

1.0.0 (2019-08-14)

  • Fully supported CLI release based on v0.10.9

0.10.9 (2019-08-05)

  • application launch: various usability improvements and bug fixes detailed below:
    • file IDs supplied to a launch command will now be auto-converted from V2 -> V1 as required
    • improved support for launching apps that use the Resource Matcher control, adding support for empty column arguments and an error if too many columns are specified
    • fix multi-select for checkbox controls with >1 option
    • respects quoting to pass argument strings containing a comma to multi-select controls
    • launching with a biosample that has multiple associated library preps will now prompt the user to choose one from a list of available options
    • added a warning when launching an app by name without also specifying --app-version

0.10.8 (2019-04-09)

  • upload dataset: retains local directory structure on remote when using the --recursive flag
  • download dataset: now downloads files in parallel for a significant speed-up when downloading many small files
  • translate dataset: fix bug when converting FASTQ datasets to samples

0.10.7 (2019-02-22)

  • new command: unlock biosample enables auto-aggregated biosamples to be used in app launches
  • new command: link file returns a signed S3 link for a given file ID
  • list appsession: add additional filters: --project-name, --project-id and --input-run
  • await appsession: add option to return appresults instead of datasets (--appresults)

0.10.6 (2019-02-11)

  • upload dataset: add --appsession-label argument to rename upload appsession
  • await appsession: fix bug in polling delayed datasets
  • all commands: rename stdout/stderr flags to --stdout / --stderr to avoid collisions with other flags

0.10.5 (2018-12-14)

  • get run: fix bug where several fields were missing

0.10.4 (2018-12-10)

  • new commands: rename application, project and appsession
  • launch application: fix bug for apps using complex TabularFieldset controls
  • await appsession: fix bug waiting for appsessions that write samples

0.10.3 (2018-11-30)

  • New commands: get / download file (by ID)
  • bs download: by default, only download what is not in the target directory already (like rsync). Use --overwrite to override
  • bs download: make project + biosample downloadable
  • bs download: fix bug where large entities (like runs) were not fully downloading
  • bs upload: fix bug where uploading a single end fastq with a validation error caused a panic

0.10.2 (2018-10-24)

  • Fix bug in bs await appsession

0.10.1 (2018-10-22)

  • Fixes compilation on Windows

0.10.0 (2018-10-22)

  • v0.10.0 release: started release notes
  • bs upload dataset:
    • Progress bars
    • Control of concurrency level
    • Ability to upload generic files --type common.files
    • Ability to ignore bad readnames in fastq files
  • New command: bs translate appresult and bs translate dataset
  • New command: bs await appsession
  • bs download: add ability to download uncompressed
  • bs application launch: Add support for TabularFieldset
  • bs create project:
    • Better output
    • Error on creating existing project
  • bs list biosample: add --projectid switch
  • bs create workflow: Slightly improve usability