Merge pull request #85 from CCBR/iss-84

fix: genome resource paths on FRCE
CCBR · Jan 9, 2024 · 5fb4d14 · 5fb4d14
2 parents a4f00c4 + a64a9b5
commit 5fb4d14
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Showing 8 changed files with 23 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,7 @@
 ## development version
 
+- Fix RSEM reference and rRNA interval list paths in FRCE-specific config files (#85, @kelly-sovacool & @slsevilla)
+
 ## v2.5.10
 
 - Fix a bug that caused slurm jobs to fail (#74, @kopardev)

diff --git a/config/genomes/frce/hg38_30.json b/config/genomes/frce/hg38_30.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/rsemref/hg38",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/hg38.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/rsemref/hg38_30",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/hg38_30.rRNA_interval_list",
             "ORGANISM": "hg38_30",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/30/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/hg38_34.json b/config/genomes/frce/hg38_34.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/rsemref/hg38",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/hg38.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/rsemref/hg38_34",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/hg38_34.rRNA_interval_list",
             "ORGANISM": "hg38_34",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/34/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/hg38_38.json b/config/genomes/frce/hg38_38.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/rsemref/hg38",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/hg38.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/rsemref/hg38_38",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/hg38_38.rRNA_interval_list",
             "ORGANISM": "hg38_38",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/38/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/hg38_41.json b/config/genomes/frce/hg38_41.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/rsemref/hg38",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/hg38.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/rsemref/hg38_41",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/hg38_41.rRNA_interval_list",
             "ORGANISM": "hg38_41",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/hg38/41/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/mm10_M21.json b/config/genomes/frce/mm10_M21.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/rsemref/mm10",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/mm10.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/rsemref/mm10_M21",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/mm10_M21.rRNA_interval_list",
             "ORGANISM": "mm10_M21",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M21/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_mm10_GRCm38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_mm10_GRCm38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_mm10_GRCm38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/mm10_M23.json b/config/genomes/frce/mm10_M23.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/rsemref/mm10",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/mm10.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/rsemref/mm10_M23",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/mm10_M23.rRNA_interval_list",
             "ORGANISM": "mm10_M23",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M23/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_mm10_GRCm38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_mm10_GRCm38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_mm10_GRCm38_v2.0.0.gff3"
         }
     }
-}
+}
diff --git a/config/genomes/frce/mm10_M25.json b/config/genomes/frce/mm10_M25.json
@@ -13,13 +13,13 @@
             "QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/qualimap_info.txt",
             "KARYOBEDS": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/karyobeds/",
             "KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/karyoplot_gene_coordinates.txt",
-            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/rsemref/mm10",
-            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/mm10.rRNA_interval_list",
+            "RSEMREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/rsemref/mm10_M25",
+            "RRNALIST": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/mm10_M25.rRNA_interval_list",
             "ORGANISM": "mm10_M25",
             "TINREF": "/mnt/projects/CCBR-Pipelines/pipelines/RENEE/resources/mm10/M25/transcripts.protein_coding_only.bed12",
             "FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_mm10_GRCm38_v2.0.0.tsv.gz",
             "FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_mm10_GRCm38_v2.0.0.tsv",
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_mm10_GRCm38_v2.0.0.gff3"
         }
     }
-}
+}