nf-core/pixelator v1.4.0

What's Changed

• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #111
• Add graph refinement options for pixelator 0.19 by @fbdtemme in #112
• Fix validation issues after nf-core/tools v3 template update by @fbdtemme in #113
• Remove --save_recovered_components options for graph outputs by @fbdtemme in #114
• Update containers for 0.19.0 by @fbdtemme in #115
• Bump version for 1.4 release by @fbdtemme in #116
• Important! Template update for nf-core/tools v3.1.0 by @nf-core-bot in #117
• Update metromap, bump conda versions by @fbdtemme in #118
• Add process_long labels to AMPLICON and COLLAPSE by @fbdtemme in #120
• Important! Template update for nf-core/tools v3.1.1 by @mirpedrol in #122
• Add manifest.contributors metadata to nextflow.config by @fbdtemme in #124
• Use environment.yml files for all conda process directives by @fbdtemme in #125
• Add nf-test tests for local modules and subworkflows by @fbdtemme in #123
• Release 1.4 by @fbdtemme in #121

Parameters

Old parameter	New parameter
	--help_full
	--show_hidden
--validationFailUnrecognisedParams
--validationLenientMode
--validationSchemaIgnoreParams
--validationShowHiddenParams
--leiden_iterations	--graph_max_refinement_recursion_depth
	--graph_max_edges_to_split
	--graph_max_edges_to_split
--save_recovered_components

Note

Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.

Software dependencies

Dependency	Old version	New version
pixelator	0.18.2	0.19.0

Note

Dependency has been updated if both old and new parameter information is present.
Dependency has been added if just the new parameter information is present.
Dependency has been removed if new parameter information isn't present.

New Contributors

• @mirpedrol made their first contribution in #122

Full Changelog: 1.3.1...1.4.0

nf-core/pixelator v1.3.1

What's Changed

• Fix conda version tag to use pixelator 0.18.2 by @fbdtemme in #107
• Patch release 1.3.1 by @fbdtemme in #108

Full Changelog: 1.3.0...1.3.1

nf-core/pixelator v1.3.0

What's Changed

• chore: sync dev after release and bump to 1.3.0dev by @fbdtemme in #95
• Make task.ext assigments closures by @fbdtemme in #96
• Update metromap to include layout step by @fbdtemme in #98
• Update citations by @fbdtemme in #97
• Chore/update readme by @ambarrio in #99
• Use R1/R2 suffixes in amplicon input fastq file renaming by @fbdtemme in #100
• Fix validation issue when using panel_file instead of panel by @fbdtemme in #101
• Restructure output folder by @fbdtemme in #102
• Make rate diff default colocalization transformation by @johandahlberg in #103
• Update pixelator to 0.18.1 by @fbdtemme in #104
• Bump version to 1.3.0 by @fbdtemme in #105
• Release pixelator 1.3.0 by @fbdtemme in #106

New Contributors

• @ambarrio made their first contribution in #99

Software versions

Software dependencies

Dependency	Old version	New version
pixelator	0.17.1	0.18.2

Note

Dependency has been updated if both old and new version information is present.
Dependency has been added if just the new version information is present.
Dependency has been removed if new version information isn't present.

Full Changelog: 1.2.0...1.3.0

nf-core/pixelator v1.2.0

What's Changed

• Template update for nf-core/tools v2.14.1 by @fbdtemme in #89
• Update pixelator to 0.17.1 by @johandahlberg in #90
• Set process_high to use 64GB of RAM and process_high_memory to use 128GB of RAM by @johandahlberg in #91
• Minor documentation fixes by @johandahlberg in #92
• Improve read renaming by @fbdtemme in #93
• Release nf-core/pixelator 1.2.0 by @fbdtemme in #94

Full Changelog: 1.1.0...1.2.0

nf-core/pixelator v1.1.0

What's Changed

• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #83
• Update to pixelator 0.16.2 by @johandahlberg in #84
• Remove a workaround for container issues, silence some warnings, update default resources by @fbdtemme in #85
• Release pixelator 1.1.0 by @fbdtemme in #86, #87

Software dependencies

Dependency	Old version	New version
pixelator	0.15.2	0.16.2

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

Full Changelog: 1.0.3...1.1.0

nf-core/pixelator v1.0.3

What's Changed

• Important! Template update for nf-core/tools v2.11 by @nf-core-bot in #74
• fix: use adapterqc output as main output of PIXELATOR_QC by @fbdtemme in #76
• fix validation issues with meta-schema by @fbdtemme in #77
• Prepare release 1.0.3 by @fbdtemme in #78
• Release 1.0.3 by @fbdtemme in #79

New Contributors

• @nf-core-bot made their first contribution in #74

Full Changelog: 1.0.2...1.0.3

nf-core/pixelator v1.0.2

[1.0.2] - 2023-11-20

Enhancements & fixes

• [PR #70] - Fix loading of absolute paths and urls in input samplesheet

nf-core/pixelator v1.0.1

[1.0.1] - 2023-10-27

Enhancements & fixes

• [PR #66] - Add a warning and workaround for singularity & apptainer
• Cleanup some linting warnings
• Update docker image in RENAME_READS to match the singularity container

Software dependencies

Dependency	Old version	New version
pixelator	0.15.0	0.15.2

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

nf-core/pixelator v1.0.0

[1.0.0] - 2023-10-17

Initial release of nf-core/pixelator.