nf-core/nanostring
An analysis pipeline for Nanostring nCounter expression data.
nanostringnanostringnorm
An incompatibility advisory with severity high has been
issued for this version of the pipeline.
See the advisory entry for more information.
Launch version 1.3.1 https://github.com/nf-core/nanostring See the advisory entry for more information.
Version history
Added
- #94 - Added nf-tests for local subworkflows
NORMALIZEandQUALITY_CONTROL. - #99 - Added nf-tests for local module
NACHO_NORMALIZE. - #100 - Added nf-tests for local module
NACHO_QC. - #101 - Added nf-tests for local module
COMPUTE_GENE_SCORES. - #102 - Added nf-tests for local module
CREATE_GENE_HEATMAP. - #103 - Added nf-tests for local module
CREATE_ANNOTATED_TABLES. - #104 - Update all nf-core modules and subworkflows.
Fixed
- #119 - Fix input channels being consumed, convert them to value channels for
CREATE_ANNOTATED_TABLESandCREATE_GENE_HEATMAP. #118
Changed
- #82 - Updated to nf-core template 3.0.2
- #95 - Add pipeline level nf-tests.
- #96 - Remove timestamp suffix from nacho_norm.R and write_out_prepared_gex.R
- #114 - Convert
CREATE_GENE_HEATMAPandCOMPUTE_GENE_SCORESto nf-core format and create a subworkflow for them. - #117 - Convert
NACHO_NORMALIZEandNACHO_QCfrom local to nf-core modules. - #122 - Updated to nf-core template 3.1.1
Dependencies
| Dependency | Old version | New version |
|---|---|---|
multiqc | 1.24.1 | 1.27 |
v1.3.0 - 2024-08-27 - Micrometre
Added
- #66 - Updated to nf-core template 2.12.1
- #71 - Updated to nf-core template 2.13.1
- #73 - Updated to nf-core template 2.14.1
Fixed
- #65 - Issue with
CREATE_GENE_HEATMAPif no list of genes was provided
Changed
- #71 - Made column
RCC_FILE_NAMEmandatory - #78 - Added Nanostring Tubemap original designfile to repository for future changes, fixed typo and removed version in picture
Dependencies
| Dependency | Old version | New version |
|---|---|---|
multiqc | 1.19 | 1.24.1 |
v1.2.0 - 2023-08-24 - Nanometre
Added
- #48 - Allow users to specify id column for heatmap #39
- #46 - Update to nf-core template
2.9 - #42 - Allow users to specify normalization method:
GEO(default) orGLM
Fixed
- #51 - Prevent HK-normalization while loading counts
- #51 - Use provided normalization method for Non-HK-normalized counts
- #46 - Publish
NACHOQC reports #44 - #47 - Update
NACHOR package including bug fix #45 - #47 - Set correct
condaenvironment forCOMPUTE_GENE_SCORESprocess
Dependencies
| Dependency | Old version | New version |
|---|---|---|
nacho | 2.0.4 | 2.0.5 |
Deprecated
v1.1.1 - 2023-06-23
Added
Fixed
- #37 - Use unique rownames for Heatmap creation
Dependencies
Deprecated
v1.0.0 - 2023-06-12 - Femtometre
Initial release of nf-core/nanostring, created with the nf-core template.
Added
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open issues
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open PRs
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last release
6 months ago
last update
6 months ago
included modules
included subworkflows
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