nf-core/nanostring

An analysis pipeline for Nanostring nCounter expression data.

nanostringnanostringnorm

Launch version 1.3.1 https://github.com/nf-core/nanostring

Version history

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`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`

Dependency	Old version	New version
`multiqc`	1.24.1	1.27

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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`

Dependency	Old version	New version
`multiqc`	1.19	1.24.1

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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`

Dependency	Old version	New version
`nacho`	2.0.5	2.0.6

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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`

Dependency	Old version	New version
`nacho`	2.0.4	2.0.5

`Deprecated`

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v1.1.1 - 2023-06-23

`Added`

#37 - Allow skipping heatmap creation #38

`Fixed`

#37 - Use unique rownames for Heatmap creation

`Dependencies`

`Deprecated`

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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`

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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

run with

See the docs on how to configure the Seqera Platform CLI.

subscribers

172

stars

14

open issues

10

open PRs

3

last release

5 months ago

last update

5 months ago

included modules

multiqc nacho_normalize nacho_qc

included subworkflows

utils_nextflow_pipeline utils_nfcore_pipeline utils_nfschema_plugin

contributors

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