Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Update doc regarding bwa_index #725

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

Merged
jfy133 merged 7 commits into from
Apr 25, 2021
Merged

Update doc regarding bwa_index #725

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
253507e
update bwa_index doc
maxibor Apr 19, 2021
7fe1501
Update nextflow_schema.json
maxibor Apr 19, 2021
0e4ef9c
update changelog
maxibor Apr 23, 2021
6709431
merge from PR
maxibor Apr 23, 2021
806e247
Update CHANGELOG.md
jfy133 Apr 25, 2021
bed1baf
Update CHANGELOG.md
jfy133 Apr 25, 2021
5fa6e53
Merge branch 'dev' into minor-doc-update
jfy133 Apr 25, 2021
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 @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed`

- Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update

### `Dependencies`

Expand Down
2 changes: 1 addition & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@
},
"bwa_index": {
"type": "string",
"description": "Path to directory containing pre-made BWA indices (i.e. everything before the endings '.amb' '.ann' '.bwt'. Most likely the same path as --fasta). If not supplied will be made for you.",
"description": "Path to directory containing pre-made BWA indices (i.e. the directory before the files ending in '.amb' '.ann' '.bwt'. Do not include the files themselves. Most likely the same directory of the file provided with --fasta). If not supplied will be made for you.",
"fa_icon": "fas fa-address-book",
"help_text": "If you want to use pre-existing `bwa index` indices, please supply the **directory** to the FASTA you also specified in `--fasta` nf-core/eager will automagically detect the index files by searching for the FASTA filename with the corresponding `bwa` index file suffixes.\n\nFor example:\n\n```bash\nnextflow run nf-core/eager \\\n-profile test,docker \\\n--input '*{R1,R2}*.fq.gz'\n--fasta 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta' \\\n--bwa_index 'results/reference_genome/bwa_index/BWAIndex/'\n```\n\n> `bwa index` does not give you an option to supply alternative suffixes/names for these indices. Thus, the file names generated by this command _must not_ be changed, otherwise nf-core/eager will not be able to find them."
},
Expand Down