nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Version history
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_componentsoptions 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_longlabels 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
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
What’s Changed
- chore: sync dev after release and bump to 1.3.0dev by @fbdtemme in #95
- Make
task.extassigments 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
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
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_highto use 64GB of RAM andprocess_high_memoryto 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
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, https:](https://github.com/nf-core/pixelator/pull/86, https:)//github.com/nf-core/pixelator/pull/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
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
[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.
[1.0.0] - 2023-10-17
Initial release of nf-core/pixelator.
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