More fixes

.markdownlint.json

@@ -0,0 +1,4 @@
+{
+    "MD013": false,
+    "MD024": { "siblings_only": true }
+}

README.md

@@ -1,9 +1,6 @@
-# [![Sarek](docs/images/Sarek_logo.png "Sarek")](https://sarek.scilifelab.se/)
-[![nf-core](docs/images/nf-core_logo.png "Sarek")](https://nf-co.re/)
+# [![Sarek](docs/images/nf-core_sarek_logo.png "Sarek")](https://sarek.scilifelab.se/)
 
-**An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing**
-
-> :warning: This pipeline is a work in progress being ported to nf-core from [SciLifeLab/Sarek](https://github/SciLifeLab/Sarek/)
+> **An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing**
 
 [![Nextflow version][nextflow-badge]](https://www.nextflow.io/)
 [![nf-core][nf-core-badge]](https://nf-co.re/)
@@ -17,7 +14,10 @@
 
 [![Join us on Slack][slack-badge]](https://nfcore.slack.com/messages/CGFUX04HZ/)
 
+> :warning: This pipeline is a work in progress being ported to nf-core from [SciLifeLab/Sarek](https://github/SciLifeLab/Sarek/)
+
 ## Introduction
+
 <img align="right" title="CAW" src="/docs/images/CAW_logo.png">
 
 Previously known as the Cancer Analysis Workflow (CAW),
@@ -32,6 +32,7 @@ Thus making installation trivial and results highly reproducible.
 It's listed on the [Elixir - Tools and Data Services Registry](https://bio.tools/Sarek), [Dockstore](https://dockstore.org/workflows/github.com/SciLifeLab/Sarek/) and [omicX - Bioinformatics tools](https://omictools.com/sarek-tool).
 
 ## Documentation
+
 The nf-core/sarek pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation](https://nf-co.re/usage/installation)
@@ -57,10 +58,12 @@ The nf-core/sarek pipeline comes with documentation about the pipeline, found in
 Sarek was developed at the [National Genomics Infastructure][ngi-link] and [National Bioinformatics Infastructure Sweden][nbis-link] which are both platforms at [SciLifeLab][scilifelab-link], with the support of [The Swedish Childhood Tumor Biobank (Barntumörbanken)][btb-link].
 
 Main authors:
+
 * [Maxime Garcia](https://github.com/MaxUlysse)
 * [Szilveszter Juhos](https://github.com/szilvajuhos)
 
 Helpful contributors:
+
 * [Johannes Alneberg](https://github.com/alneberg)
 * [Phil Ewels](https://github.com/ewels)
 * [Jesper Eisfeldt](https://github.com/J35P312)
@@ -87,21 +90,20 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 * [CHANGELOG](CHANGELOG.md)
 
 ## Aknowledgements
+
 [![Barntumörbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken-0) | [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)
 :-:|:-:
 [![National Genomics Infrastructure](docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/) | [![National Bioinformatics Infrastructure Sweden](docs/images/NBIS_logo.png)](https://nbis.se)
 
-
 ## Citation
 
 If you use nf-core/sarek for your analysis, please cite the `Sarek` pre-print as follows:
-Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, de Ståhl TD, Wirta V, Nistér M, Nystedt B, Käller M. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants**. *bioRxiv*. 2018. p. 316976. [doi: 10.1101/316976](https://www.biorxiv.org/content/10.1101/316976v1).
+> Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, de Ståhl TD, Wirta V, Nistér M, Nystedt B, Käller M. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants**. *bioRxiv*. 2018. p. 316976. [doi: 10.1101/316976](https://www.biorxiv.org/content/10.1101/316976v1).
 
 You can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.2582812](https://doi.org/10.5281/zenodo.2582812)
 
 You can cite the `nf-core` pre-print as follows:
-Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v3).
-
+> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v3).
 
 [bioconda-badge]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?logo=data:image/png;base64,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
 [btb-link]: https://ki.se/forskning/barntumorbanken-0

conf/igenomes.config

@@ -10,32 +10,32 @@
  params {
    genomes {
      'GRCh37' {
-       acLoci           = "${params.igenomes_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
-       acLociGC         = "${params.igenomes_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
-       bwaIndex         = "${params.igenomes_base}/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
-       dbsnp            = "${params.igenomes_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf"
-       dbsnpIndex       = "${params.igenomes_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
-       genomeDict       = "${params.igenomes_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
-       genomeFile       = "${params.igenomes_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
-       genomeIndex      = "${params.igenomes_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
-       intervals        = "${params.igenomes_base}/Annotation/intervals/wgs_calling_regions_CAW.list"
-       knownIndels      = "${params.igenomes_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
-       knownIndelsIndex = "${params.igenomes_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
+       acLoci           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
+       acLociGC         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
+       bwaIndex         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
+       dbsnp            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf"
+       dbsnpIndex       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
+       genomeDict       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
+       genomeFile       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
+       genomeIndex      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
+       intervals        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_CAW.list"
+       knownIndels      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
+       knownIndelsIndex = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
        snpeffDb         = "GRCh37.75"
        vepCacheVersion  = "95"
      }
      'GRCh38' {
-       acLoci           = "${params.igenomes_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
-       acLociGC         = "${params.igenomes_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
-       bwaIndex         = "${params.igenomes_base}/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
-       dbsnp            = "${params.igenomes_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
-       dbsnpIndex       = "${params.igenomes_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
-       genomeDict       = "${params.igenomes_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
-       genomeFile       = "${params.igenomes_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
-       genomeIndex      = "${params.igenomes_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
-       intervals        = "${params.igenomes_base}/Annotation/intervals/wgs_calling_regions.hg38.bed"
-       knownIndels      = "${params.igenomes_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
-       knownIndelsIndex = "${params.igenomes_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
+       acLoci           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
+       acLociGC         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
+       bwaIndex         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
+       dbsnp            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
+       dbsnpIndex       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
+       genomeDict       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
+       genomeFile       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
+       genomeIndex      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
+       intervals        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
+       knownIndels      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
+       knownIndelsIndex = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
        snpeffDb         = "GRCh38.86"
        vepCacheVersion  = "95"
      }

docs/annotation.md

@@ -3,6 +3,7 @@
 ## Tools
 
 With Sarek, annotation is done using `snpEff`, `VEP`, or even both consecutively:
+
 - `--tools snpEff`
   - To annotate using `snpEff`
 - `--tools VEP`
@@ -32,6 +33,7 @@ You need to specify the cache directory using `--snpEff_cache` and `--vep_cache`
 The cache will only be used when `--annotation_cache` and cache directories are specified (either in command lines or in a configuration file).
 
 Example:
+
 ```bash
 nextflow run nf-core/sarek/main.nf --tools snpEff --step annotate --sample file.vcf.gz --snpEff_cache /Path/To/snpEffCache --annotation_cache
 nextflow run nf-core/sarek/main.nf --tools VEP --step annotate --sample file.vcf.gz --vep_cache /Path/To/vepCache --annotation_cache
@@ -40,11 +42,13 @@ nextflow run nf-core/sarek/main.nf --tools VEP --step annotate --sample file.vcf
 ## Using VEP CADD plugin
 
 To enable the use of the VEP CADD plugin:
- - Download the CADD files
- - Specify them (either on the command line, like in the example or in a configuration file)
- - use the `--cadd_cache` flag
+
+- Download the CADD files
+- Specify them (either on the command line, like in the example or in a configuration file)
+- use the `--cadd_cache` flag
 
 Example:
+
 ```bash
 nextflow run nf-core/sarek/main.nf --step annotate --tools VEP --sample file.vcf.gz --cadd_cache \
     --cadd_InDels /PathToCADD/InDels.tsv.gz \
@@ -57,16 +61,19 @@ nextflow run nf-core/sarek/main.nf --step annotate --tools VEP --sample file.vcf
 
 An helper script has been designed to help downloading CADD files.
 Such files are meant to be share between multiple users, so this script is mainly meant for people administrating servers, clusters and advanced users.
+
 ```bash
 nextflow run build.nf --cadd_cache /Path/To/CADDcache --cadd_version <CADD version> --genome <GENOME>
 ```
 
 ## Using VEP GeneSplicer plugin
 
 To enable the use of the VEP GeneSplicer plugin:
- - use the `--genesplicer` flag
+
+- use the `--genesplicer` flag
 
 Example:
-```
+
+```bash
 nextflow run annotate.nf --tools VEP --sample file.vcf.gz --genesplicer
 ```