Add marmoset genome and add rule to reformat GTFs missing attributes

.pre-commit-config.yaml

@@ -4,7 +4,8 @@ exclude: |
   (?x)(
       ^assets/|
       ^docs/.*.html|
-      ^_extensions/
+      ^_extensions/|
+      ^tests/data/
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 - Fix spelling of shared SIF directory on biowulf -- it is `/data/CCBR_Pipeliner/SIFs` with a lowercase "s" at the end. (#182, @kelly-sovacool)
 - Raise an error if too few reads are left after trimming with cutadapt. (#184, @kelly-sovacool)
+- Reformat GTF files during `renee build` that are missing 'gene_biotype' or 'gene_type' attributes in exons. (#185, @kelly-sovacool)
+- Add support for the marmoset genome (mCalJac1 2021). (#185, @kelly-sovacool)
 
 ## RENEE 2.6.3
 

config/cluster.json

@@ -51,7 +51,8 @@
         "time": "1-00:00:00"
     },
     "qualimapinfo": {
-        "mem": "20g"
+        "mem": "20g",
+        "time": "1:00:00"
     },
     "rsem": {
         "gres": "lscratch:500",
@@ -120,5 +121,9 @@
     },
     "trim_se": {
         "threads": "32"
+    },
+    "reformat_gtf": {
+        "mem": "20g",
+        "time": "1:00:00"
     }
 }

config/containers/images.json

@@ -5,6 +5,7 @@
         "base": "docker://nciccbr/ccbr_ubuntu_22.04:v4",
         "bbtools": "docker://nciccbr/ccbr_bbtools_38.87:v0.0.1",
         "build_rnaseq": "docker://nciccbr/ccbr_build_rnaseq:v0.0.1",
+        "build_gtf": "docker://nciccbr/ccbr_build_rnaseq:v2",
         "cutadapt": "docker://nciccbr/ccbr_cutadapt_1.18:v032219",
         "fastq_screen": "docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0",
         "fastqc": "docker://nciccbr/ccbr_fastqc_0.11.9:v1.1",

config/genomes/biowulf/mCalJac1_2021.json

@@ -0,0 +1,22 @@
+{
+    "references": {
+        "rnaseq": {
+            "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/GCF_011100555.1_mCalJa1.2.pat.X_genomic.fna",
+            "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/GCF_011100555.1_mCalJa1.2.pat.X_genomic.fna",
+            "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/GCF_011100555.1_mCalJa1.2.pat.X_genomic.gtf.reformat.gtf",
+            "GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/STAR/2.7.6a/genome",
+            "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/annotate.genes.txt",
+            "ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/annotate.isoforms.txt",
+            "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/refFlat.txt",
+            "BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/genes.ref.bed",
+            "GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/geneinfo.bed",
+            "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/qualimap_info.txt",
+            "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/karyobeds/",
+            "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/karyoplot_gene_coordinates.txt",
+            "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/rsemref/mCalJac1_2021",
+            "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/mCalJac1_2021.rRNA_interval_list",
+            "ORGANISM": "mCalJac1",
+            "TINREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mCalJac1_2021/transcripts.protein_coding_only.bed12"
+        }
+    }
+}

docs/RNA-seq/Resources.md

@@ -9,19 +9,20 @@ The hg38 fasta files were downloaded from the GDC with virus and decoy sequences
 while these sequences were manually added to the hg19 fasta from Encode.
 See details here: <https://github.com/CCBR/build-renee-refs>
 
-| **Genome** | **Species**          | **Annotation Version**                                                                 | **Notes**                                                                                       |
-| ---------- | -------------------- | -------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------- |
-| hg19_19    | Homo sapiens (human) | [Gencode Release 19](https://www.gencodegenes.org/human/release_19.html)               | [GRCh37](https://www.gencodegenes.org/human/release_19.html), Annotation Release date: 07/2013  |
-| hg19_36    | Homo sapiens (human) | [Gencode Release 36-lift-37](https://www.gencodegenes.org/human/release_36lift37.html) | [GRCh37](https://www.gencodegenes.org/human/release_36lift37.html)                              |
-| hg38_30    | Homo sapiens (human) | [Gencode Release 30](https://www.gencodegenes.org/human/release_30.html)               | [GRCh38](https://www.gencodegenes.org/human/release_30.html), Annotation Release date: 11/2018  |
-| hg38_34    | Homo sapiens (human) | [Gencode Release 34](https://www.gencodegenes.org/human/release_34.html)               | [GRCh38](https://www.gencodegenes.org/human/release_34.html), Annotation Release date: 04/2020  |
-| hg38_36    | Homo sapiens (human) | [Gencode Release 36](https://www.gencodegenes.org/human/release_36.html)               | [GRCh38](https://www.gencodegenes.org/human/release_36.html), Annotation Release date: 05/2020  |
-| hg38_38    | Homo sapiens (human) | [Gencode Release 38](https://www.gencodegenes.org/human/release_38.html)               | [GRCh38](https://www.gencodegenes.org/human/release_38.html), Annotation Release date: 05/2021  |
-| hg38_41    | Homo sapiens (human) | [Gencode Release 41](https://www.gencodegenes.org/human/release_41.html)               | [GRCh38](https://www.gencodegenes.org/human/release_41.html), Annotation Release date: 07/2022  |
-| hg38_45    | Homo sapiens (human) | [Gencode Release 45](https://www.gencodegenes.org/human/release_45.html)               | [GRCh38](https://www.gencodegenes.org/human/release_45.html), Annotation Release date: 03/2023  |
-| mm10_M21   | Mus musculus (mouse) | [Gencode Release M21](https://www.gencodegenes.org/mouse/release_M21.html)             | [GRCm38](https://www.gencodegenes.org/mouse/release_M21.html), Annotation Release date: 04/2019 |
-| mm10_M23   | Mus musculus (mouse) | [Gencode Release M23](https://www.gencodegenes.org/mouse/release_M23.html)             | [GRCm38](https://www.gencodegenes.org/mouse/release_M23.html), Annotation Release date: 09/2019 |
-| mm10_M25   | Mus musculus (mouse) | [Gencode Release M25](https://www.gencodegenes.org/mouse/release_M25.html)             | [GRCm38](https://www.gencodegenes.org/mouse/release_M25.html), Annotation Release date: 04/2020 |
+| **Genome**    | **Species**                                    | **Annotation Version**                                                                           | **Notes**                                                                                       |
+| ------------- | ---------------------------------------------- | ------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------- |
+| hg19_19       | Homo sapiens (human)                           | [Gencode Release 19](https://www.gencodegenes.org/human/release_19.html)                         | [GRCh37](https://www.gencodegenes.org/human/release_19.html), Annotation Release date: 07/2013  |
+| hg19_36       | Homo sapiens (human)                           | [Gencode Release 36-lift-37](https://www.gencodegenes.org/human/release_36lift37.html)           | [GRCh37](https://www.gencodegenes.org/human/release_36lift37.html)                              |
+| hg38_30       | Homo sapiens (human)                           | [Gencode Release 30](https://www.gencodegenes.org/human/release_30.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_30.html), Annotation Release date: 11/2018  |
+| hg38_34       | Homo sapiens (human)                           | [Gencode Release 34](https://www.gencodegenes.org/human/release_34.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_34.html), Annotation Release date: 04/2020  |
+| hg38_36       | Homo sapiens (human)                           | [Gencode Release 36](https://www.gencodegenes.org/human/release_36.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_36.html), Annotation Release date: 05/2020  |
+| hg38_38       | Homo sapiens (human)                           | [Gencode Release 38](https://www.gencodegenes.org/human/release_38.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_38.html), Annotation Release date: 05/2021  |
+| hg38_41       | Homo sapiens (human)                           | [Gencode Release 41](https://www.gencodegenes.org/human/release_41.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_41.html), Annotation Release date: 07/2022  |
+| hg38_45       | Homo sapiens (human)                           | [Gencode Release 45](https://www.gencodegenes.org/human/release_45.html)                         | [GRCh38](https://www.gencodegenes.org/human/release_45.html), Annotation Release date: 03/2023  |
+| mm10_M21      | Mus musculus (mouse)                           | [Gencode Release M21](https://www.gencodegenes.org/mouse/release_M21.html)                       | [GRCm38](https://www.gencodegenes.org/mouse/release_M21.html), Annotation Release date: 04/2019 |
+| mm10_M23      | Mus musculus (mouse)                           | [Gencode Release M23](https://www.gencodegenes.org/mouse/release_M23.html)                       | [GRCm38](https://www.gencodegenes.org/mouse/release_M23.html), Annotation Release date: 09/2019 |
+| mm10_M25      | Mus musculus (mouse)                           | [Gencode Release M25](https://www.gencodegenes.org/mouse/release_M25.html)                       | [GRCm38](https://www.gencodegenes.org/mouse/release_M25.html), Annotation Release date: 04/2020 |
+| mCalJac1_2021 | Callithrix jacchus (white-tufted-ear marmoset) | [Genome assembly mCalJa1.2.pat.X](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) | Annotation release date: 04/2021                                                                |
 
 You can run `renee run --help` to view the most up-to-date list of genome annotations available in your installation of RENEE.
 

pyproject.toml

@@ -36,8 +36,11 @@ classifiers = [
 requires-python = ">=3.11"
 dependencies = [
     "argparse",
+    "biopython",
     "ccbr_tools@git+https://github.com/CCBR/[email protected]",
     "Click >= 8.1.3",
+    "HTSeq",
+    "numpy",
     "PySimpleGui < 5",
     "snakemake >= 7.32, < 8"
 ]