spatialvi

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Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...

nf-core-bot

Use `to_legacy_anndata` function from `spatialdata_io` instead of custom code

1

### Description of feature We are currently using custom code as a work-around as a replacement for the `to_legacy_anndata` function from `spatialdata_io`, which did not exist when the work with...

fasterius

Add MultiQC report

13

### Description of feature Having individual QC reports for each sample is nice, but it would be cool to have one aggregated report that gives an overview of all samples...

grst

Aggregate samples into single object

4

### Description of feature Would be nice to have a single object instead of inidividual h5ad files. Optional batch correction for integration.

grst

### Description of feature Once spaceranger is fully implemented, the "full-size" test dataset should be updated to run the workflow incl. spaceranger.

grst

### Description of the bug When launching this workflow : ```sh nextflow run nf-core/spatialvi -r dev \ -profile docker \ --input /shared/samplesheet_spaceranger.csv \ --spaceranger_probeset /shared/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv \ --spaceranger_reference /shared/homo_sapiens_chr22_reference.tar.gz \ --qc_min_counts...

AlanLonguet

### Description of feature Hi! Thanks for the work on the pipeline! I wonder if you ever considered adding the possibility to add the [--unknown-slide](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/slide-info) parameter to the `spaceranger count`...

pstorozenko

Add quality control metrics as MultiQC custom content

1

This PR adds the quality controls metrics from the report to MultiQC as custom content. Additionally, the way the metrics are presented in the report are harmonised to be shown...

fasterius

Report sample names

1

This PR changes the subtitle of the final reports to contain the sample name, which was something that was lacking before.

fasterius

No `fastq_dir` specified or no samples found in folder. Output into S3//

1

### Description of the bug Hello, thanks for the great pipeline. I am trying to run the test profile with the workDir set to an S3 bucket. The untar of...

LucFrancisENX