From 892da3d31800fb11c5961026e1588c2560f92b22 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 6 Aug 2024 14:55:46 +0000 Subject: [PATCH] [automated] Fix code linting --- README.md | 4 ++-- docs/output.md | 32 +++++++++++++++----------------- docs/usage.md | 46 +++++++++++++++++++++++----------------------- modules.json | 2 +- 4 files changed, 41 insertions(+), 43 deletions(-) diff --git a/README.md b/README.md index 94ba71342e..0743b6a9ac 100644 --- a/README.md +++ b/README.md @@ -54,7 +54,7 @@ Depending on the options and samples provided, the pipeline can currently perfor - `freebayes` - `GATK HaplotypeCaller` - `Manta` - - IndexCov + - IndexCov - `mpileup` - `MSIsensor-pro` - `Mutect2` @@ -170,7 +170,7 @@ We thank the following people for their extensive assistance in the development - [pallolason](https://github.com/pallolason) - [Paul Cantalupo](https://github.com/pcantalupo) - [Phil Ewels](https://github.com/ewels) -- [Pierre Lindenbaum][https://github.com/lindenb= +- [Pierre Lindenbaum]https://github.com/lindenb= - [Sabrina Krakau](https://github.com/skrakau) - [Sam Minot](https://github.com/sminot) - [Sebastian-D](https://github.com/Sebastian-D) diff --git a/docs/output.md b/docs/output.md index 37b0969084..124f333f25 100644 --- a/docs/output.md +++ b/docs/output.md @@ -581,23 +581,21 @@ The output is scaled to around 1. So a long stretch with values of 1.5 would be **Output directory: `{outdir}/variantcalling/indexcov/`** -In addition to the interactive HTML files, `indexcov` outputs a number of text files: - -+ `$prefix-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found. - the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes. - `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples. - `bins.lo`: number of bins with value < 0.15. high values indicate missing data. - `bins.hi`: number of bins with value > 1.15. - `bins.in`: number of bins with value inside of (0.85, 1.15) - `p.out`: `bins.out/bins.in` - `PC1...PC5`: PCA projections calculated with depth of autosomes. - -+ `$prefix-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the - proportion of 16KB blocks at or above that scaled coverage value. -+ `$prefix-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there - scaled coverage for that sample in that 16KB chunk. - - +In addition to the interactive HTML files, `indexcov` outputs a number of text files: + +- `$prefix-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found. + the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes. + `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples. + `bins.lo`: number of bins with value < 0.15. high values indicate missing data. + `bins.hi`: number of bins with value > 1.15. + `bins.in`: number of bins with value inside of (0.85, 1.15) + `p.out`: `bins.out/bins.in` + `PC1...PC5`: PCA projections calculated with depth of autosomes. + +- `$prefix-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the + proportion of 16KB blocks at or above that scaled coverage value. +- `$prefix-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there + scaled coverage for that sample in that 16KB chunk. #### Manta diff --git a/docs/usage.md b/docs/usage.md index fa12faa6ee..b87bab44b6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -838,30 +838,30 @@ nextflow run nf-core/sarek --known_indels false --genome GRCh38.GATK For GATK.GRCh38 the links for each reference file and the corresponding processes that use them is listed below. For GATK.GRCh37 the files originate from the same sources: -| File | Tools | Origin | Docs | -| :-------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------- | -| ascat_alleles | ASCAT | https://www.dropbox.com/s/uouszfktzgoqfy7/G1000_alleles_hg38.zip | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS | -| 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` | | -| 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 | -| fasta | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Indexcov, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, 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 | +| File | Tools | Origin | Docs | +| :-------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------- | +| ascat_alleles | ASCAT | https://www.dropbox.com/s/uouszfktzgoqfy7/G1000_alleles_hg38.zip | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS | +| 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` | | +| 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 | +| fasta | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Indexcov, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, 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 | | fasta_fai | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Indexcov, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, 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 | -| germline_resource | GetPileupsummaries,Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| germline_resource_tbi | GetPileupsummaries,Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| intervals | ApplyBQSR(Spark), ASCAT, Baserecalibrator(Spark), BCFTools, CNNScoreVariants, ControlFREEC, Deepvariant, FilterVariantTranches, FreeBayes, GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Strelka, mpileup, MSISensorPro, Mutect2, VCFTools | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| known_indels | BaseRecalibrator(Spark), FilterVariantTranches | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| known_indels_tbi | BaseRecalibrator(Spark), FilterVariantTranches | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| known_snps | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | -| known_snps_tbi | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | -| mappability | ControlFREEC | http://xfer.curie.fr/get/vyIi4w8EONl/out100m2_hg38.zip | http://boevalab.inf.ethz.ch/FREEC/tutorial.html | -| pon | Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- | -| pon_tbi | Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- | +| germline_resource | GetPileupsummaries,Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| germline_resource_tbi | GetPileupsummaries,Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| intervals | ApplyBQSR(Spark), ASCAT, Baserecalibrator(Spark), BCFTools, CNNScoreVariants, ControlFREEC, Deepvariant, FilterVariantTranches, FreeBayes, GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Strelka, mpileup, MSISensorPro, Mutect2, VCFTools | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| known_indels | BaseRecalibrator(Spark), FilterVariantTranches | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| known_indels_tbi | BaseRecalibrator(Spark), FilterVariantTranches | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| known_snps | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | | +| known_snps_tbi | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | +| mappability | ControlFREEC | http://xfer.curie.fr/get/vyIi4w8EONl/out100m2_hg38.zip | http://boevalab.inf.ethz.ch/FREEC/tutorial.html | +| pon | Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- | +| pon_tbi | Mutect2 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- | ## How to customise SnpEff and VEP annotation diff --git a/modules.json b/modules.json index 9c48a82f35..9ef6a5c996 100644 --- a/modules.json +++ b/modules.json @@ -309,7 +309,7 @@ "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", "installed_by": ["modules"] }, - "goleft/indexcov": { + "goleft/indexcov": { "branch": "master", "git_sha": "a941aa24517960d7b9eeab4c3a5adfb3f70a5e4b", "installed_by": ["modules"]