Add minimal genomes possibilities

.github/workflows/ci-extra.yml

@@ -3,6 +3,27 @@ name: sarek extra CI
 on: [push, pull_request]  
 
 jobs:
+  minimal:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        genome: [smallerGRCh37, minimalGRCh37]
+        intervals: [--no_intervals, '']
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+        env:
+          NXF_VER: '19.10.0'
+      - name: Download image
+        run: |
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
+      - name: Run test
+        run: |
+          nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
   profile:
     runs-on: ubuntu-18.04
     strategy:
@@ -15,7 +36,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          NXF_VER: '19.04.0'
+          NXF_VER: '19.10.0'
       - name: Download image
         run: |
           docker pull nfcore/sarek:dev
@@ -35,7 +56,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          NXF_VER: '19.04.0'
+          NXF_VER: '19.10.0'
       - name: Download image
         run: |
           docker pull nfcore/sarek:dev
@@ -56,7 +77,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          NXF_VER: '19.04.0'
+          NXF_VER: '19.10.0'
       - name: Download image
         run: |
           docker pull nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        nxf_ver: ['19.04.0', '']
+        nxf_ver: ['19.10.0', '']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

.travis.yml

@@ -30,7 +30,7 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.10.0' # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:

CHANGELOG.md

@@ -11,6 +11,12 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#45](https://github.com/nf-core/sarek/pull/45) - Include Workflow figure in `README.md`
 - [#46](https://github.com/nf-core/sarek/pull/46) - Add location to abstracts
 - [#52](https://github.com/nf-core/sarek/pull/52) - Add support for mouse data `GRCm38`
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add `no_intervals` params
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add automatic generation of `intervals` file with `BuildIntervals` process
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add minimal support for minimal genome (only `fasta`, or `fasta` + `knownIndels`)
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add new processes (`IndexBamFile`, `IndexBamRecal`) to deal with optional usage of interval files and minimal genome
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add tests for minimal genome usage
+- [#60](https://github.com/nf-core/sarek/pull/60) - Add new minimal genomes (`TAIR10`, `EB2`, `UMD3.1`, `bosTau8`, `WBcel235`, `ce10`, `CanFam3.1`, `canFam3`, `GRCz10`, `danRer10`, `BDGP6`, `dm6`, `EquCab2`, `equCab2`, `EB1`, `Galgal4`, `galGal4`, `Gm01`, `hg38`, `hg19`, `Mmul_1`, `mm10`, `IRGSP-1.0`, `CHIMP2.1.4`, `panTro4`, `Rnor_6.0`, `rn6`, `R64-1-1`, `sacCer3`, `EF2`, `Sbi1`, `Sscrofa10.2`, `susScr3`, `AGPv3`) to `igenomes.config`
 - [#61](https://github.com/nf-core/sarek/pull/61) - Add params `split_fastq`
 - [#61](https://github.com/nf-core/sarek/pull/61) - Add test `SPLITFASTQ`
 
@@ -25,6 +31,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#41](https://github.com/nf-core/sarek/pull/41), [#55](https://github.com/nf-core/sarek/pull/55) - Update `tiddit` from `2.7.1` to `2.8.1`
 - [#41](https://github.com/nf-core/sarek/pull/41) - Update `vcfanno` from `0.3.1` to `0.3.2`
 - [#54](https://github.com/nf-core/sarek/pull/54) - Bump version to `2.5.2dev`
+- [#60](https://github.com/nf-core/sarek/pull/60) - Some process (`BaseRecalibrator`, `ApplyBQSR`, `Mpileup`) have now optional usage of interval files
+- [#60](https://github.com/nf-core/sarek/pull/60) - Update documentation
 - [#71](https://github.com/nf-core/sarek/pull/71) - Update `README`
 - [#71](https://github.com/nf-core/sarek/pull/71) - Update `CHANGELOG`
 

README.md

@@ -2,7 +2,7 @@
 
 > **An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing**
 
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
 [![nf-core](https://img.shields.io/badge/nf--core-pipeline-brightgreen.svg)](https://nf-co.re/)
 [![DOI](https://zenodo.org/badge/184289291.svg)](https://zenodo.org/badge/latestdoi/184289291)
 

conf/genomes.config

@@ -26,8 +26,8 @@ params {
       knownIndels           = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       knownIndelsIndex      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
       snpeffDb              = 'GRCh37.75'
-      vepCacheVersion       = '95'
       species               = 'homo_sapiens'
+      vepCacheVersion       = '95'
     }
     'GRCh38' {
       acLoci                = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
@@ -46,36 +46,25 @@ params {
       knownIndels           = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       knownIndelsIndex      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
       snpeffDb              = 'GRCh38.86'
-      vepCacheVersion       = '95'
       species               = 'homo_sapiens'
+      vepCacheVersion       = '95'
+    }
+    'minimalGRCh37' {
+      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
     }
     'smallGRCh37' {
-      acLoci                = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
-      acLociGC              = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci.gc"
       dbsnp                 = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
       fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
       germlineResource      = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
       intervals             = "${params.genomes_base}/small.intervals"
       knownIndels           = ["${params.genomes_base}/1000G_phase1.indels.b37.small.vcf.gz", "${params.genomes_base}/Mills_and_1000G_gold_standard.indels.b37.small.vcf.gz"]
       snpeffDb              = 'GRCh37.75'
-      vepCacheVersion       = '95'
       species               = 'homo_sapiens'
+      vepCacheVersion       = '95'
     }
-    'GRCm38' {
-      bwaIndex              = "${params.genomes_base}/genome.fa.{amb,ann,bwt,pac,sa}"
-      chrDir                = "${params.genomes_base}/Chromosomes"
-      chrLength             = "${params.genomes_base}/GRCm38.len"
-      dbsnp                 = "${params.genomes_base}/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
-      dbsnpIndex            = "${params.genomes_base}/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
-      dict                  = "${params.genomes_base}/genome.dict"
-      fasta                 = "${params.genomes_base}/genome.fa"
-      fastaFai              = "${params.genomes_base}/genome.fa.fai"
-      intervals             = "${params.genomes_base}/GRCm38_calling_list.bed"
-      knownIndels           = "${params.genomes_base}/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
-      knownIndelsIndex      = "${params.genomes_base}/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
-      snpeffDb              = 'GRCm38.86'
-      vepCacheVersion       = '98'
-      species               = 'mus_musculus'
+    'smallerGRCh37' {
+      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
+      knownIndels           = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
     }
   }
 }

conf/igenomes.config

@@ -26,8 +26,8 @@ params {
       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'
       species                = 'homo_sapiens'
+      vepCacheVersion        = '95'
     }
     'GRCh38' {
       acLoci                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
@@ -46,8 +46,8 @@ params {
       knownIndels            = "${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       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
       snpeffDb               = 'GRCh38.86'
-      vepCacheVersion        = '95'
       species                = 'homo_sapiens'
+      vepCacheVersion        = '95'
     }
     'GRCm38' {
       bwaIndex               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
@@ -62,8 +62,144 @@ params {
       knownIndels            = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
       knownIndelsIndex       = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
       snpeffDb               = 'GRCm38.86'
-      vepCacheVersion        = '98'
       species                = 'mus_musculus'
+      vepCacheVersion        = '98'
+    }
+    'TAIR10' {
+      bwaIndex               = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'EB2' {
+      bwaIndex               = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'UMD3.1' {
+      bwaIndex               = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'bosTau8' {
+      bwaIndex               = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'WBcel235' {
+      bwaIndex               = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'ce10' {
+      bwaIndex               = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'CanFam3.1' {
+      bwaIndex               = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'canFam3' {
+      bwaIndex               = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'GRCz10' {
+      bwaIndex               = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'danRer10' {
+      bwaIndex               = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'BDGP6' {
+      bwaIndex               = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'dm6' {
+      bwaIndex               = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'EquCab2' {
+      bwaIndex               = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'equCab2' {
+      bwaIndex               = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'EB1' {
+      bwaIndex               = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Galgal4' {
+      bwaIndex               = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'galGal4' {
+      bwaIndex               = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Gm01' {
+      bwaIndex               = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'hg38' {
+      bwaIndex               = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'hg19' {
+      bwaIndex               = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Mmul_1' {
+      bwaIndex               = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'mm10' {
+      bwaIndex               = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'IRGSP-1.0' {
+      bwaIndex               = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'CHIMP2.1.4' {
+      bwaIndex               = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'panTro4' {
+      bwaIndex               = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Rnor_6.0' {
+      bwaIndex               = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'rn6' {
+      bwaIndex               = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'R64-1-1' {
+      bwaIndex               = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'sacCer3' {
+      bwaIndex               = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'EF2' {
+      bwaIndex               = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Sbi1' {
+      bwaIndex               = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'Sscrofa10.2' {
+      bwaIndex               = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'susScr3' {
+      bwaIndex               = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+    }
+    'AGPv3' {
+      bwaIndex               = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
+      fasta                  = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
     }
   }
 }