curationpretext - 1.4.2 - UNSC Nereid (H2)

What's Changed

• Fix to GENERATECRAMCSV (by @mahesh-panchal)
  • Missing quotations in the shell script would stop some CRAM data from being taken into account.
• Update to test data paths for Sanger local testing.
• Corrected spelling of track value.
• Added GNU_SORT memory allocation of 1Gb.

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.4.1...1.4.2

- Nextflow
Published by DLBPointon about 1 year ago

curationpretext - 1.4.1 - UNSC Nereid (H1)

What's Changed

• Template update to 3.2.1
• Updated the CI testing to better match nf-core ci/cd.
• Added run_hires to switch on/off hires pretextmap generation.
• modules.config had an explicit enabled = true for pretext*ingest steps - this made it seem like no output was generated from the pipeline.
• In production it looks like this was actually stopping output from that module from being output from the module.
• NF-Schema is now 2.3.0.

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.4.0...1.4.1

- Nextflow
Published by DLBPointon about 1 year ago

curationpretext - 1.4.0 - UNSC Nereid

What's Changed

• Fixed bug where occasionally and when using minimap2 as the aligner, the pipeline would run both bwamem2 and minimap2 mapping subworkflow (fixes issue #93)
• Updated contributors list to include their ORCID.
• Added --skip_tracks to control which tracks to generate, useful in cases where the end user may have no longread_data and must skip coverage generation. This can be set to "ALL" to only generate the pretext maps.
• Removed a number of processes which are no longer in use.
• Updated tests to account for all output files.
• Updated all modules to most recent on nf-core.
• Update modules and base config files for parity with TreeVal (large genome optimisations).
• Update the PretextGraph version.

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.3.2...1.4.0

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.3.2 - UNSC Pillar-of-Autumn (H2)

What's Changed

• Patch issue with lowercased assemblies - telo subworkflow will now force the whole sequence into uppercase before Telo_finding.
• Two GAWK modules added to support the above
• Minor bugs with Pretext_graph modules where gap and telomere were not being ingested.

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.3.1...1.3.2

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.3.1 - UNSC Pillar-of-Autumn (H1)

What's Changed

• Change bai to csi for more flexible indexing by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/85
• Release 1.3.1 - UNSC Pillar-of-Autumn H1 by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/86

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.3.0...1.3.1

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.3.0 - UNSC Pillar-of-Autumn

Major Changes include:

• Update to Template version 3.2.
• PIPELINE_INITIALISATION now initialises the channels for the pipeline.
• all_output flag, which, by default, will only output the post-processed pretext files.
• Deleted the PRETEXTINGESTION subworkflow, replaced with a direct call to the PRETEXTGRAPH module.
• Updated PRETEXT_GRAPH for better logic and to match the same update to TreeVal.
• Inputs to pretext graph are now optional/conditional depending on runs from previous steps.
• Updated NF_TEST config to ignore modules and subworkflows.
• Updated modules.config to reflect all the above changes.
• Updated nextflow.config to cleanup by default -- previously this was added as a profile.
  • Aim to add NF-BOOST in an upcoming H release.
• We no longer use the avg or log coverage tracks, processes related to these have been removed.
• Shell blocks have been replaced with script blocks.
• Removed the MAPS_ONLY entry point, entry points are being deprecated, and the subworkflow is not used.
  • This can be re-added on request.
• Replaced 5 modules with GAWK to remove bad practice (cat > sed commands).
• Replaced all nf-core with sanger-tol https://github.com/sanger-tol/curationpretext/pull/80
• Added sanger-tol branding https://github.com/sanger-tol/curationpretext/pull/81
  • Re-organised subworkflows and modules to the current standard of subworkflows/local/SUBWORKFLOW/main.nf and modules/local/TOOL/SUBTOOL/main.nf https://github.com/sanger-tol/curationpretext/pull/82

With thanks to: @muffato and @prototaxites for help with this release.

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.2.0

What's Changed

• Update to Pretext (0.0.8) to fix bugs in graph ingestion by @DLBPointon
  
• Adding NF-Test by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/51
• Curationpretext updates by @mahesh-panchal in https://github.com/sanger-tol/curationpretext/pull/52
• Update schema so input can only be of included values by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/59
• Comments by yy5 by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/69
• 1.2.0 - UNSC Spirit-of-Fire by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/65

New Contributors

• @mahesh-panchal made their first contribution in https://github.com/sanger-tol/curationpretext/pull/52

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.1.0...1.2.0

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.1.0 - UNSC Delphi

What's Changed

• Updated NF-core modules to remove Defaults conda.
• Spelling corrections
• Corrected Citations and Changelog
• Fixes to CICD
• Added the Zenodo Code

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/1.0.1...1.1.0

- Nextflow
Published by DLBPointon over 1 year ago

curationpretext - 1.0.1 - UNSC Cradle H1

Hot Fix 1 for UNSC Cradle - This adds support for end users selecting whether pretext maps are sorted or not. - Containerises find_telomere

- Nextflow
Published by DLBPointon almost 2 years ago

curationpretext - 1.0.0

What's Changed

• Update generatecramcsv.nf by @scorreard in https://github.com/sanger-tol/curationpretext/pull/15
• Updating all modules by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/18
• updating documents also caught bug that was stopping params file from being imported correctly by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/19
• updated docs by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/20
• Updating everything by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/17
• Merging histories of main by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/27
• Linting for release by @muffato in https://github.com/sanger-tol/curationpretext/pull/29
• conf/test_full.config by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/30
• Pre-v1 merge by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/28

New Contributors

• @scorreard made their first contribution in https://github.com/sanger-tol/curationpretext/pull/15
• @muffato made their first contribution in https://github.com/sanger-tol/curationpretext/pull/29

Full Changelog: https://github.com/sanger-tol/curationpretext/compare/0.1.0...1.0.0

- Nextflow
Published by DLBPointon about 2 years ago

curationpretext - v0.1.0 - UNSC Infinity

What's Changed

• Master by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/1
• Updates to complete pipeline, only waiting on hr snapshot which curre… by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/2
• Main by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/3
• Updates to configs and md by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/4
• Adding linting fixes by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/5
• Dlb pointon patch 1 by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/10
• Update CITATIONS.md by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/11
• Fix for schema by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/13
• Adding CHANGELOG by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/14
• The Big Merge by @DLBPointon in https://github.com/sanger-tol/curationpretext/pull/12

New Contributors

• @DLBPointon made their first contribution in https://github.com/sanger-tol/curationpretext/pull/1

Full Commitlog: https://github.com/sanger-tol/curationpretext/commits/v0.1.0 Full Changelog: https://github.com/sanger-tol/curationpretext/CHANGELOG.md

- Nextflow
Published by DLBPointon over 2 years ago