add starIndex

nf-core · Dec 4, 2024 · cd59ed7 · cd59ed7
1 parent 236b168
commit cd59ed7
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Showing 123 changed files with 135 additions and 1 deletion.
diff --git a/assets/generate_yaml_asset.sh b/assets/generate_yaml_asset.sh
@@ -75,7 +75,7 @@ do
     echo "  bowtie2_index: \"${i}/\"" >> igenomes/${species}/${genome}/${build}.yml
 done
 
-# All source BWAmem1
+# Just first source BWAmem1 (not keeping version0.5.x or version0.6.0 for now)
 cat ngi-igenomes_file_manifest.txt | grep "BWAIndex" | grep -v "version" | rev | cut -d "/" -f 2- | rev | sort -u > all_bwaindex.txt
 
 for i in `cat all_bwaindex.txt`;
@@ -111,5 +111,17 @@ do
     echo "  dragmap_hashtable: \"${i}/\"" >> igenomes/${species}/${genome}/${build}.yml
 done
 
+# All source star
+cat ngi-igenomes_file_manifest.txt | grep "STARIndex" | rev | cut -d "/" -f 2- | rev | sort -u > all_star.txt
+
+for i in `cat all_star.txt`;
+do
+    species=$(echo $i | cut -d "/" -f 5)
+    genome=$(echo $i | cut -d "/" -f 6)
+    build=$(echo $i | cut -d "/" -f 7)
+
+    echo "  star_index: \"${i}/\"" >> igenomes/${species}/${genome}/${build}.yml
+done
+
 #  Homo_sapiens/GATK/GRCh37.yml should actually be Homo_sapiens/GATK/GRCh37decoy.yml
 mv igenomes/Homo_sapiens/GATK/GRCh37.yml igenomes/Homo_sapiens/GATK/GRCh37decoy.yml
diff --git a/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml b/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml b/assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/STARIndex/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/NCBI/TAIR10.yml b/assets/igenomes/Arabidopsis_thaliana/NCBI/TAIR10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Arabidopsis_thaliana/NCBI/build9.1.yml b/assets/igenomes/Arabidopsis_thaliana/NCBI/build9.1.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/STARIndex/"
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
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bacillus_subtilis_168/Ensembl/EB2.yml b/assets/igenomes/Bacillus_subtilis_168/Ensembl/EB2.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/Ensembl/Btau_4.0.yml b/assets/igenomes/Bos_taurus/Ensembl/Btau_4.0.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/Ensembl/UMD3.1.yml b/assets/igenomes/Bos_taurus/Ensembl/UMD3.1.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/Btau_4.2.yml b/assets/igenomes/Bos_taurus/NCBI/Btau_4.2.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/Btau_4.6.1.yml b/assets/igenomes/Bos_taurus/NCBI/Btau_4.6.1.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.1.yml b/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.1.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.yml b/assets/igenomes/Bos_taurus/NCBI/UMD_3.1.yml
@@ -7,3 +7,4 @@
   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/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau4.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau4.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau6.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau6.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau7.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau7.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/STARIndex/"
diff --git a/assets/igenomes/Bos_taurus/UCSC/bosTau8.yml b/assets/igenomes/Bos_taurus/UCSC/bosTau8.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS210.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS210.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS220.yml b/assets/igenomes/Caenorhabditis_elegans/Ensembl/WS220.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/NCBI/WS190.yml b/assets/igenomes/Caenorhabditis_elegans/NCBI/WS190.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/NCBI/WS195.yml b/assets/igenomes/Caenorhabditis_elegans/NCBI/WS195.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/UCSC/ce10.yml b/assets/igenomes/Caenorhabditis_elegans/UCSC/ce10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Caenorhabditis_elegans/UCSC/ce6.yml b/assets/igenomes/Caenorhabditis_elegans/UCSC/ce6.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/Ensembl/BROADD2.yml b/assets/igenomes/Canis_familiaris/Ensembl/BROADD2.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/Ensembl/CanFam3.1.yml b/assets/igenomes/Canis_familiaris/Ensembl/CanFam3.1.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/NCBI/build2.1.yml b/assets/igenomes/Canis_familiaris/NCBI/build2.1.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/NCBI/build3.1.yml b/assets/igenomes/Canis_familiaris/NCBI/build3.1.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/UCSC/canFam2.yml b/assets/igenomes/Canis_familiaris/UCSC/canFam2.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/STARIndex/"
diff --git a/assets/igenomes/Canis_familiaris/UCSC/canFam3.yml b/assets/igenomes/Canis_familiaris/UCSC/canFam3.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/Ensembl/GRCz10.yml b/assets/igenomes/Danio_rerio/Ensembl/GRCz10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/Ensembl/Zv9.yml b/assets/igenomes/Danio_rerio/Ensembl/Zv9.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/NCBI/GRCz10.yml b/assets/igenomes/Danio_rerio/NCBI/GRCz10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/NCBI/Zv9.yml b/assets/igenomes/Danio_rerio/NCBI/Zv9.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/UCSC/danRer10.yml b/assets/igenomes/Danio_rerio/UCSC/danRer10.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
diff --git a/assets/igenomes/Danio_rerio/UCSC/danRer7.yml b/assets/igenomes/Danio_rerio/UCSC/danRer7.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25.yml b/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.yml b/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP6.yml b/assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP6.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/NCBI/build4.1.yml b/assets/igenomes/Drosophila_melanogaster/NCBI/build4.1.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/NCBI/build5.3.yml b/assets/igenomes/Drosophila_melanogaster/NCBI/build5.3.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.3/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.3/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.3/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.3/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/NCBI/build5.41.yml b/assets/igenomes/Drosophila_melanogaster/NCBI/build5.41.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.41/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.41/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.41/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5.41/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/NCBI/build5.yml b/assets/igenomes/Drosophila_melanogaster/NCBI/build5.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build5/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/UCSC/dm3.yml b/assets/igenomes/Drosophila_melanogaster/UCSC/dm3.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm3/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm3/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm3/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm3/Sequence/STARIndex/"
diff --git a/assets/igenomes/Drosophila_melanogaster/UCSC/dm6.yml b/assets/igenomes/Drosophila_melanogaster/UCSC/dm6.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
diff --git a/assets/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28.yml b/assets/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Enterobacteriophage_lambda/NCBI/1993-04-28/Sequence/STARIndex/"
diff --git a/assets/igenomes/Equus_caballus/Ensembl/EquCab2.yml b/assets/igenomes/Equus_caballus/Ensembl/EquCab2.yml
@@ -7,3 +7,4 @@
   bowtie1_index: "s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BowtieIndex/"
   bowtie2_index: "s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
   bwamem1_index: "s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/"
+  star_index: "s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"