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Merge pull request #1556 from asp8200/update_usage_md
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Updating usage.md
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@asp8200
asp8200 authored Jun 10, 2024
2 parents 66e98ca + a2ecdcb commit 54b3b08
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1 change: 1 addition & 0 deletions CHANGELOG.md
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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`

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6 changes: 3 additions & 3 deletions docs/usage.md
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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 |
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