From 7a8d4db030f5534c90bdf4be5f8a6c8238bc829d Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 10 Jun 2024 14:11:28 +0000 Subject: [PATCH 1/2] Adding some ticks around some commands --- docs/usage.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index f39e327bb1..d12361f9fb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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 | From a2ecdcb98c0c28f22ba45f369190614de3e1c473 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 10 Jun 2024 14:15:49 +0000 Subject: [PATCH 2/2] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c231616998..25b58f0f41 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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