Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove double image in the README #72

Open
wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

Remove double image in the README #72

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ Special thanks to the following for their contributions to the release:
- [PR #60](https://github.com/nf-core/fastquorum/pull/60) - Enable automatic escalation of memory for FilterConsensusReads.
- [PR #67](https://github.com/nf-core/fastquorum/pull/67) - Fix setting the parameters from igenomes.
- [PR #68](https://github.com/nf-core/fastquorum/pull/68) - Temporary fix to merging BAMs across lanes in template-coordinate order. Using `fgbio SortBam` after `samtools merge`. Related to [samtools#2062](https://github.com/samtools/samtools/pull/2062).
- [PR #72](https://github.com/nf-core/fastquorum/pull/72) - Fix image in README

## [[1.0.0]](https://github.com/nf-core/fastquorum/releases/tag/1.0.0) -- 2024-05-20

Expand Down
4 changes: 1 addition & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/fastquorum/results).

| Tools | Description |
| ------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------- |
| <p align="center"><img title="Fastquorum Workflow (Tools)" src="docs/images/fastquorum_subway.png" width=100%></p> | <p align="center"><img title="Fastquorum Workflow (Description)" src="docs/images/fastquorum_subway.desc.png" width=100%></p> |
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

These are actually different images. The left hand side, "Tools", fastquorum_subway.png lists the tool names and the right hand side, "Description", fastquorum_subway.desc.png describes what those tools do at each step.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Mmm, I don't see the reason to have both to be honest.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It feels a little redundant because most of the tools have descriptive names, but I can appreciate the intention to clarify what each is doing. We can discuss further when Nils is back, but I don't see this as a needed change for the release.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Fine, we can release without changing this

<p align="center"><img title="Fastquorum Workflow (Description)" src="docs/images/fastquorum_subway.desc.png" width=100%></p>

1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Fastq to BAM, extracting UMIs ([`fgbio FastqToBam`](http://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html))
Expand Down
Loading