Harshil Patel

### Description of bug Providing `data_format: "yaml"` via the standard `multiqc_config.yaml` is not working. However, providing the equivalent option via the CLI `-k yaml` is working fine. This could be...

Looks like it might be due to the image not being created properly from the website during the nf-core sync process because the same logo was created here: https://github.com/nf-core/chipseq/blob/nf-core-template-merge-2.4/docs/images/nf-core-chipseq_logo_dark.png

Find test dataset where PRESEQ doesn't fail

1

Related to https://github.com/nf-core/rnaseq/issues/544

Add IDR analysis

5

Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines: https://github.com/kundajelab/atac-seq-pipeline https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit Another implementation in NF: https://github.com/DoaneAS/atacflow ENCODE ATAC-seq Guidelines: https://www.encodeproject.org/atac-seq/ Amongst other...

### Description of feature See https://github.com/nf-core/rnaseq/issues/828#issuecomment-1135673459

This should be possible via the suggested implementation in [this issue](https://github.com/CGATOxford/UMI-tools/issues/465). The flow will be very similar to what we are doing with STAR/Salmon.

### Description of feature [Homepage](https://github.com/OceanGenomics/mudskipper) [Bioconda](https://bioconda.github.io/recipes/mudskipper/README.html?highlight=mudskipper#package-package%20'mudskipper') Currently, we don't have a native quantification method for HISAT2 genomic alignments because we need to project these onto transcriptomic alignments for accurate quantification...

Add tin.py output to MultiQC report

2

When adding the `rseqc/tin` the TIN files are being found by MultiQC (v1.11) but I can't seem to be able to get rid of the `markdup.sorted.bam` extension as shown in...

Add pseudo-alignment via Kallisto

3

We already have an option to perform pseudo-alignment with Salmon but it would be great to have a similar workflow that uses Kallisto instead. I am hoping we can recycle...

See https://github.com/nf-core/rnaseq/pull/264 I think this is something maybe we can revisit when we convert this pipeline to DSL2 @heuermh ? Will close the open PR for now in favour of...