Three very minor typos are present in these documents that break the code when copied-and-pasted as they are.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056484652-Typos-in-docs

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1.  https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants

the fifth code block on this page

fastp will overwrite -o without checking if it is the same as -i. Worth adding a check for this scenario.

This would make the process for making small corrections easier for non-developers. From a comment on #8349.

This should be pretty easy to do and a good task for a new developer or community member looking to make a small contribution.

• Search whether this issue (or a similar issue) has been solved before
  using the search tab above. Link the previous issue if appropriate below.

• Paste your deepTools version (deeptools --version) and your python
  version (python --version) below.
  deeptools 3.3.2
  Python 3.6.0

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  (ignore if you simply sp

The current implementation of slice md5 validation proceeds in two steps; it first tries to validate the md5 for the entire slice span. If that fails, it falls back to checking the md5 for a smaller span ([terminating one base earlier](https://github.com/

We'd love to consider your Circos plots for inclusion in the training materials as examples of what it can do and the variety of outputs!

So please, comment share your plot here with your Galaxy history, or [send us an email](mailto:helena.rasche@gmail.com?subject=Circos%20Plot%20for%20Tr

From Nikolas:

"The last lines of the tutorial with the tSNE embedding don't quite work out of the box. You may want to substitute with the following:

tSNE.pagoda <- Rtsne(cell.clustering$distance,is_distance=T,initial_dims=100,perplexity=10)

embed.tSNE <- tSNE.pagoda$Y

rownames(embed.tSNE) <- cell.clustering$clustering$labels

app <- make.pagoda.app(tamr2, tam, varinfo, go.env, pwpca

Our current UMI pipelines tend to involve going to uBAMs with UMIs in them, then using a chain of picard SamToFastq | bwa or other aligner | MergeBamAlignment. Both of the picard tools have grown in complexity over the years, and can be quite intimidating for folks who haven't used them before. In addition the need to sort BAMs into htsjdk-queryname order adds an extra time-consuming sort to t

When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O.

Following from this it would be convenient to have a stripSeqQual function that replaces the two fields with *.

Clarify what the known adapters file is for (a database of adapters that can be referenced by name), and how it differs from specifying an adapter file to one of the -a/-g/-b options.

bioconvert/bioconvert#210 (comment)

can the anaconda3 installation documentation be modified to reflect the above comment?

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

conda update -n base -c defaults conda -y
conda update --all -y
# python 3.

the description in man/Pagoda2-class.rd is not sufficient (getKnnClusters and getEmbedding are not mentioned)? where can I get a complete description of Pagoda2?

and perhaps conda

Describe the bug
When trying to download *.txt document from the pipeline DOCUMENTS tab - the downloaded file contains error instead of the document content

To Reproduce
Steps to reproduce the behavior:

1. Open any pipeline, select the DOCUMENTS tab
2. Upload the document with txt extension
3. Click the Download button next to the uploaded document (or click the doc