Added

• #94 - Added nf-tests for local subworkflows NORMALIZE and QUALITY_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_TABLES and CREATE_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_HEATMAP and COMPUTE_GENE_SCORES to nf-core format and create a subworkflow for them.
• #117 - Convert NACHO_NORMALIZE and NACHO_QC from local to nf-core modules.
• #122 - Updated to nf-core template 3.1.1

Dependencies

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_HEATMAP if no list of genes was provided

Changed

• #71 - Made column RCC_FILE_NAME mandatory
• #78 - Added Nanostring Tubemap original designfile to repository for future changes, fixed typo and removed version in picture

Dependencies

v1.2.1 - 2024-01-18 - Nanometre

Added

• #55 - Added the Bioinformatics publication to the citation list
• #55 - Updated to nf-core template 2.11.1
• #58 - Granularized the containers for NACHO and Heatmaps

Dependencies

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) or GLM

Fixed

• #51 - Prevent HK-normalization while loading counts
• #51 - Use provided normalization method for Non-HK-normalized counts
• #46 - Publish NACHO QC reports #44
• #47 - Update NACHO R package including bug fix #45
• #47 - Set correct conda environment for COMPUTE_GENE_SCORES process

Dependencies

Deprecated

v1.1.1 - 2023-06-23

Added

• #37 - Allow skipping heatmap creation #38

Fixed

• #37 - Use unique rownames for Heatmap creation

Dependencies

Deprecated

v1.1.0 - 2023-06-22 - Picometre

Added

• #33 - Add functionality to generate gene-count heatmaps #17
• #32 - Add functinoality to compute gene scores #16

Fixed

Dependencies

Deprecated

v1.0.0 - 2023-06-12 - Femtometre

Initial release of nf-core/nanostring, created with the nf-core template.

Added

• #21 - Add quality control using NACHO #11
• #21 - Add normalization with and without Housekeeping genes using NACHO #12
• #21 - Add tests and respective test data #19
• #23 - Add tables with non-housekeeping-normalized counts to MultiQC report