add bwamem1

nf-core · Dec 4, 2024 · ecd0c72 · ecd0c72
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diff --git a/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml b/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+- genome: "TAIR10"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/"
+- genome: "TAIR10"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.5.x/"
+- genome: "TAIR10"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml b/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/Bowtie2Index/"
+- genome: "TAIR9"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BWAIndex/"
+- genome: "TAIR9"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BWAIndex/version0.5.x/"
+- genome: "TAIR9"
+  source: "Ensembl"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/NCBI/TAIR10.yml b/assets/igenomes/Arabidopsis_thaliana/NCBI/TAIR10.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/Bowtie2Index/"
+- genome: "TAIR10"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BWAIndex/"
+- genome: "TAIR10"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BWAIndex/version0.5.x/"
+- genome: "TAIR10"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/NCBI/build9.1.yml b/assets/igenomes/Arabidopsis_thaliana/NCBI/build9.1.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/Bowtie2Index/"
+- genome: "build9.1"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/BWAIndex/"
+- genome: "build9.1"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/BWAIndex/version0.5.x/"
+- genome: "build9.1"
+  source: "NCBI"
+  species: "Arabidopsis_thaliana"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13.yml b/assets/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/Bowtie2Index/"
+- genome: "2004-02-13"
+  source: "NCBI"
+  species: "Bacillus_cereus_ATCC_10987"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/BWAIndex/"
+- genome: "2004-02-13"
+  source: "NCBI"
+  species: "Bacillus_cereus_ATCC_10987"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/BWAIndex/version0.5.x/"
+- genome: "2004-02-13"
+  source: "NCBI"
+  species: "Bacillus_cereus_ATCC_10987"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bacillus_subtilis_168/Ensembl/EB2.yml b/assets/igenomes/Bacillus_subtilis_168/Ensembl/EB2.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+- genome: "EB2"
+  source: "Ensembl"
+  species: "Bacillus_subtilis_168"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/"
+- genome: "EB2"
+  source: "Ensembl"
+  species: "Bacillus_subtilis_168"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.5.x/"
+- genome: "EB2"
+  source: "Ensembl"
+  species: "Bacillus_subtilis_168"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/Ensembl/Btau_4.0.yml b/assets/igenomes/Bos_taurus/Ensembl/Btau_4.0.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/Bowtie2Index/"
+- genome: "Btau_4.0"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/BWAIndex/"
+- genome: "Btau_4.0"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/BWAIndex/version0.5.x/"
+- genome: "Btau_4.0"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/Ensembl/UMD3.1.yml b/assets/igenomes/Bos_taurus/Ensembl/UMD3.1.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+- genome: "UMD3.1"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/"
+- genome: "UMD3.1"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.5.x/"
+- genome: "UMD3.1"
+  source: "Ensembl"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/Btau_4.2.yml b/assets/igenomes/Bos_taurus/NCBI/Btau_4.2.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/Bowtie2Index/"
+- genome: "Btau_4.2"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/BWAIndex/"
+- genome: "Btau_4.2"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/BWAIndex/version0.5.x/"
+- genome: "Btau_4.2"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/Btau_4.6.1.yml b/assets/igenomes/Bos_taurus/NCBI/Btau_4.6.1.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/Bowtie2Index/"
+- genome: "Btau_4.6.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/BWAIndex/"
+- genome: "Btau_4.6.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/BWAIndex/version0.5.x/"
+- genome: "Btau_4.6.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.1.yml b/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.1.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/Bowtie2Index/"
+- genome: "UMD_3.1.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/"
+- genome: "UMD_3.1.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.5.x/"
+- genome: "UMD_3.1.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.yml b/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/Bowtie2Index/"
+- genome: "UMD_3.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/BWAIndex/"
+- genome: "UMD_3.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/BWAIndex/version0.5.x/"
+- genome: "UMD_3.1"
+  source: "NCBI"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau4.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau4.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/Bowtie2Index/"
+- genome: "bosTau4"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BWAIndex/"
+- genome: "bosTau4"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BWAIndex/version0.5.x/"
+- genome: "bosTau4"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau6.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau6.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/Bowtie2Index/"
+- genome: "bosTau6"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BWAIndex/"
+- genome: "bosTau6"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BWAIndex/version0.5.x/"
+- genome: "bosTau6"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau7.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau7.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/Bowtie2Index/"
+- genome: "bosTau7"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BWAIndex/"
+- genome: "bosTau7"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BWAIndex/version0.5.x/"
+- genome: "bosTau7"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau8.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau8.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+- genome: "bosTau8"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/"
+- genome: "bosTau8"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.5.x/"
+- genome: "bosTau8"
+  source: "UCSC"
+  species: "Bos_taurus"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/Bowtie2Index/"
+- genome: "WBcel215"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BWAIndex/"
+- genome: "WBcel215"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BWAIndex/version0.5.x/"
+- genome: "WBcel215"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+- genome: "WBcel235"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/"
+- genome: "WBcel235"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.5.x/"
+- genome: "WBcel235"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS210.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS210.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/Bowtie2Index/"
+- genome: "WS210"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BWAIndex/"
+- genome: "WS210"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BWAIndex/version0.5.x/"
+- genome: "WS210"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS220.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS220.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/Bowtie2Index/"
+- genome: "WS220"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BWAIndex/"
+- genome: "WS220"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BWAIndex/version0.5.x/"
+- genome: "WS220"
+  source: "Ensembl"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/NCBI/WS190.yml b/assets/igenomes/Caenorhabditis_elegans/NCBI/WS190.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/Bowtie2Index/"
+- genome: "WS190"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BWAIndex/"
+- genome: "WS190"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BWAIndex/version0.5.x/"
+- genome: "WS190"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/NCBI/WS195.yml b/assets/igenomes/Caenorhabditis_elegans/NCBI/WS195.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/Bowtie2Index/"
+- genome: "WS195"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BWAIndex/"
+- genome: "WS195"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BWAIndex/version0.5.x/"
+- genome: "WS195"
+  source: "NCBI"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BWAIndex/version0.6.0/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/UCSC/ce10.yml b/assets/igenomes/Caenorhabditis_elegans/UCSC/ce10.yml
@@ -6,3 +6,15 @@
   fasta_dict: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.dict"
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+- genome: "ce10"
+  source: "UCSC"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/"
+- genome: "ce10"
+  source: "UCSC"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.5.x/"
+- genome: "ce10"
+  source: "UCSC"
+  species: "Caenorhabditis_elegans"
+  bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"