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

Updating usage.md #1556

Merged
merged 2 commits into from
Jun 10, 2024
Merged

Updating usage.md #1556

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7a8d4db
Adding some ticks around some commands
asp8200 Jun 10, 2024
a2ecdcb
Update changelog
asp8200 Jun 10, 2024
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 @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
- [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
- [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
- [#1556](https://github.com/nf-core/sarek/pull/1556) - Fix display of some commands in `docs/usage.md`

### Removed

Expand Down
6 changes: 3 additions & 3 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -831,9 +831,9 @@ For GATK.GRCh38 the links for each reference file and the corresponding processe
| ascat_loci | ASCAT | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS |
| ascat_loci_gc | ASCAT | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS |
| ascat_loci_rt | ASCAT | https://www.dropbox.com/s/xlp99uneqh6nh6p/RT_G1000_hg38.zip | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS |
| bwa | bwa-mem | bwa index -p bwa/${fasta.baseName} $fasta | |
| bwamem2 | bwa-mem2 | bwa-mem2 index -p bwamem2/${fasta} $fasta | |
| dragmap | DragMap | dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap | |
| bwa | bwa-mem | `bwa index -p bwa/${fasta.baseName} $fasta` | |
| bwamem2 | bwa-mem2 | `bwa-mem2 index -p bwamem2/${fasta} $fasta` | |
| dragmap | DragMap | `dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap` | |
| dbsnp | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle |
| dbsnp_tbi | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | |
| dict | Baserecalibrator(Spark), CNNScoreVariant, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, MarkDulpicates(Spark), MergeVCFs, Mutect2, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle |
Expand Down
Loading