Move documentation from old branch #160
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
JoseEspinosa
approved these changes
Dec 4, 2024
CHANGELOG.md
Outdated
Comment on lines
16
to
31
| - Add option to use Dayhoff encoding for sourmash. | ||
| - Add `bam2fasta` process to kmermaid pipeline and flags involved. | ||
| - Add `extract_coding` and `peptide_bloom_filter` process and flags involved. | ||
| - Add `track_abundance` feature to keep track of hashed kmer frequency. | ||
| - Add social preview image | ||
| - Add `fastp` process for trimming reads | ||
| - Add option to use compressed `.tgz` file containing output from 10X Genomics' `cellranger count` outputs, including `possorted_genome_bam.bam` and `barcodes.tsv` files | ||
| - Add samtools_fastq_unaligned and samtools_fastq_aligned process for converting bam to per cell | ||
| barcode fastq | ||
| - Add version printing for sencha, bam2fasta, and sourmash in Dockerfile, update versions in environment.yml | ||
| - For processes translate, sourmash compute add cpus=1 as they are only serial ([#107](https://github.com/nf-core/kmermaid/pull/107)) | ||
| - Add `sourmash sig merge` for aligned/unaligned signatures from bam files, and add `--skip_sig_merge` option to turn it off | ||
| - Add `--protein_fastas` option for creating sketches of already-translated protein sequences | ||
| - Add `--skip_compare option` to skip `sourmash_compare_sketches` process | ||
| - Add merging of aligned/unaligned parts of single-cell data ([#117](https://github.com/nf-core/kmermaid/pull/117)) | ||
| - Add renamed package dependency orpheum (used to be known as sencha) |
There was a problem hiding this comment.
Some sentence end with point and some other not, might be better to be consistent
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Moved some documentation from the old pipeline. No other files are worth including at this point. The documentation will require additional changes but these will be introduced after the new implementation is written.
PR checklist
docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).