v0.6.0

• Can parse metadata.json generated from WDLs with nested scatters
• Added pytest for testing parsing WDLs with subworkflows and nested scatters

v0.5.2

Bug fixes

• Graphviz-related error (FileNotfoundError for .dot or .dot.svg)
• Fix MIME type for HTML reports on GCS bucket.
  • Can click on HTML file on a GCS bucket and web browsers will correctly recognize it as a valid HTML.

v0.5.1

Fixed bugs

• Unnecessary indentation in HTML. Web browsers couldn't recognize it as a valid HTML.

Added pre-commit.

v0.5.0

Support for WDL struct and subworkflows.

• e.g. ENCODE DNase-seq pipeline

More index variables up to 7 layer nested scatter/subworkflow in WDL.

• i, j, k -> i, j, k, l, m, o, p

v0.4.2.1

Fix dependency in setup.py.

v0.4.2

Use miniwdl to parse WDL's meta {} section.
Fix importing bug.

v0.4.1.1

Fix dependency problem.

v0.4.0

• Important notice
  • UCSC browser web page no longer accepts long URL (where full track hub text is encoded in such URL). So instead, Croo makes another alternative link with a linked track hub txt file instead of a full track hub text. One issue is that this text file should be public. So this track hub txt file will be converted into public URL (according to parameters defined by users). e.g. being presigned on GCS.

We have replaced old localization module (Caper's CaperURI) with a new one (Autouri's AutoURI).

• Deprecated parameters

  • --http-user and --http-password: Autouri automatically uses ~/.netrc file for authentication of HTTP URLs. Use ~/.netrc file.
  • --use-gsutil-over-aws-s3: Old module used aws s3 CLI for S3 files and gsutil for GCS files. This parameter is no longer needed since new model uses Python interfaces instead of CLIs.

• Added parameters

  • --verbose (-V) and --debug (-D): Prints detailed logs. verbose >= INFO, debug >= DEBUG.
  • --use-gsutil-for-s3: This is different from the deprecated parameter --use-gsutil-over-aws-s3. Old loc module used gsutil CLI for file transfer between GCS (gs://) and any other. But new module optionally (controlled by this parameter) uses gsutil only for direct file transfer between GCS and S3 (s3://). If this flag is turned on gsutil will be used only for such direct file transfer.

• Bug fixes

  • --tmp_dir was not checked correctly (when it's on $CWD).
  • --no-graph: This has been removed, Croo will automatically check if dot executable exists on $PATH. This is a bit annoying since pip install graphviz does not install this important executable dot. Users can only get it with system-level installation command like sudo apt-get install graphviz.

v0.3.4

Bug fixes

• Fix for TypeError: 'NoneType' object is not iterable error.

v0.3.2

Added --no-graph to disable the task graph feature.

• Fix for issue #11

Added graphviz to pip package requirements.

• So that graphviz is automatically installed during pip installation
• However, pip install graphviz still doesn't install GraphViz's executable dot.
  • Debian/Ubuntu: sudo apt-get install graphviz