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CHANGELOG.md

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Changelog

[0.9.1] 2024-12-24

  • Minor code cleanup

[0.9.0] 2024-12-23

  • Only supports Nextflow 24.10 and later (uses Groovy 4)
  • Shift to quiltcore 0.1.6 convenience methods
  • Shift metadata and configuration to quilt scope of nextflow.config
  • Moved test workflows into wf folder
  • Write the output URI when publishing
  • Improve handling of dynamically-specified URIs
  • Rewrite README.md, splitting out developer documentation to README_DEV.md

[0.8.12] 2024-12-03 UNPUBLISHED

  • Extract flags and metadata from nextflow.config
  • Remove unused methods and keys
  • Remove support for propertyName
  • Use IntelliJ to fix types and lint

[0.8.11] 2024-11-5 UNPUBLISHED

  • Catch all toJson errors

[0.8.10] 2024-11-4 UNPUBLISHED

  • Ignore publish to 'home'
  • Fix: Cannot set property 'package_id' on null object

[0.8.9] 2024-10-31 UNPUBLISHED

  • Handle multiple/internal publishDir calls

[0.8.8] 2024-10-31 UNPUBLISHED

  • Debug build

[0.8.7] 2024-10-23 UNPUBLISHED

  • Use package cache instead of params to find output URIs (in order to support dynamic URIs set by, e.g. main.nf)
  • Allow setting metadata from inside the workflow

[0.8.6] 2024-09-11

  • Fix addOverlay bug on subfolders
  • Fix Windows tests
  • Improve test coverage

[0.8.5] 2024-09-10a

  • Error with packaging subfolders on S3 overlay
  • Improved overlay debugging

[0.8.4] 2024-09-10

  • Fix bug with unrecognized output URIs

[0.8.3] 2024-09-08

  • Fix Windows bug with overlay files

[0.8.2] 2024-09-07

  • Use copyFile rather than writeString for overlay files [requires NextFlow 23 or later]
  • Restore README and quilt_summarize to output

[0.8.1] 2024-09-05

  • Get output URI directly from params
  • Add dest parameter to Quilt URIs inferred from S3 URIs
  • Specify outputPrefixes using quilt section of nextflow.config
  • Stop proactively installing packages

[0.8.0] 2024-08-31

  • Add and improve code coverage using jacoco
  • Support S3 URIs as an overlay plugin
  • Fix bug with pathless input URIs

[0.7.17] UNRELEASED

  • support ChunkedChecksums

[0.7.16] 2024-06-17

  • use prior package, if any, for relative paths

[0.7.15] 2024-06-17

  • use null bucket for relative paths (e.g., nf-schema)

[0.7.14] 2024-06-14

  • improve package name debugging

[0.7.13] 2024-06-13

  • catch (java.nio.file.NoSuchFileException e) on deinstall

[0.7.12] 2024-05-16

  • Fix getFileName()
  • Pin PACKAGE_URL for examples/hurdat

[0.7.11] 2024-05-14 UNOFFICIAL

  • Republish correctly

[0.7.10] 2024-05-10 FAILED TO UPLOAD

  • Debug build of QuiltCore-Java
  • Fail when pushing to read-only buckets

[0.7.9] 2024-01-30

  • Auto-install (needed for < 23.12?)

[0.7.8] 2024-01-30 UNOFFICIAL

  • Add debugging for installs

[0.7.7] 2024-01-24 UNOFFICIAL

  • Properly implement and test getFilename()
  • Install package just before download
  • Add and pass path-input integration test
  • Add unit test for "&path=" Quilt+ URIs

[0.7.6] 2024-01-10 UNOFFICIAL

  • Re-enable crash on failure

[0.7.5] 2023-10-17

  • Grab all multiqc subfolders

[0.7.4] 2023-10-16b UNOFFICIAL

  • Actually print the exception stack trace
  • make install to enable nextflow testing

[0.7.3] 2023-10-16a UNOFFICIAL

  • Catch and log exception on push failure

[0.7.2] 2023-10-16 UNOFFICIAL

  • Throw exceptions on push failure

[0.7.1] 2023-10-15

[0.7.0] 2023-10-05

  • Officially QuiltCore 0.1.0 instead of Python

[0.6.0] 2023-10-03 UNOFFICIAL

(interim release still using Python)

  • Stop overwriting README.md (use README_NF_QUILT.md instead)
    • improve formatting
  • Smarter quilt_summarize.json
    • Top level (only): md, html, pdf, csv, tsv
    • multiqc sub-folder HTML

[0.5.0] 2023-09-04 UNOFFICIAL

  • Switch to quiltcore-java [NOTE: this pre-release does NOT check workflows]
  • Do not pre-install packages (only install before write)

[0.4.5] 2023-08-23

  • fix metadata in README.md
  • write out nf-quilt/*.json files
  • add summarize wildcards (md, html) for QuiltProduct
  • redo normalizedPaths
  • reduce logging (especially stack traces and filesystem calls)
  • convert non-fatal errors to warnings

[0.4.4] 2023-08-22

  • JDK 11 compatibility (i.e., remove stripIndent)
  • Add parameter to skip README and metadata (default is to include both)
  • Improve test coverage of metadata and QuiltProduct

[0.4.3] 2023-08-04

  • Do not publish Quilt package unless workflow succeeds
  • [or the metadata specifies &force=true]

[0.4.2] 2023-07-02

  • Fix normalizePath test (return exact match, else last de-pathed match)
  • Skip creating README.md if zero-length string

[0.4.1] 2023-06-02

Beta release (not yet on nextflow-io/plugins)

  • Only match unpinned packages for normalizePath
  • Append to README.md if it exists

[0.4.0] 2023-05-19

  • Use msg fragment parameter as commit message when writing packages
  • Removed Benchling support (will add back in a future release)
  • Don't crash when writing to Quilt+ URIs with &path= fragments (by ignoring that part)

[0.3.5] 2023-04-05

  • Runs on >=22.10.6

[0.3.4] 2023-04-04

  • Alpha: Call Benchling API after publishing package
  • accept "?commit_message=text+string&readme=GString" in Quilt+ URI
  • Support Nextflow 23+

[0.3.3] 2023-03-08

  • Fail gracefully on quilt3 errors
  • Detailed Nextflow Tower instructions
  • Call quilt3 during integration tests
  • Add full Quilt+ URL support, including metadata in query string

[0.3.2] 2023-02-24