Helixer

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.1
+current_version = 0.7.1
 commit = True
 tag = True
 

annotation/__init__.py

@@ -7,7 +7,7 @@
 from Mikado.parsers import parser_factory
 from Mikado.transcripts import Gene, Transcript
 
-VERSION = '0.6.1'
+VERSION = '0.7.1'
 RUN_METADATA = "run_details.json"
 
 UTR_SELECTION_OPTIONS = ('augustus', 'gold', 'silver', 'bronze', 'all', 'hq_assembly', 'lq_assembly')

annotation/prediction.py

@@ -59,6 +59,9 @@ def combine_arguments_prediction(cli_arguments):
     if cli_arguments.repeats:
         cromwell_inputs['ei_prediction.repeats_gff'] = cli_arguments.repeats.name
 
+    if cli_arguments.helixer_model:
+        cromwell_inputs['ei_prediction.helixer_model'] = cli_arguments.helixer_model
+
     if cli_arguments.force_train:
         cromwell_inputs['ei_prediction.force_train'] = cli_arguments.force_train
 
@@ -89,6 +92,9 @@ def combine_arguments_prediction(cli_arguments):
     if cli_arguments.mikado_utr_files:
         cromwell_inputs['ei_prediction.mikado_utr_files'] = ' '.join(cli_arguments.mikado_utr_files)
 
+    if cli_arguments.temp_dir:
+        cromwell_inputs['ei_prediction.temp_dir'] = cli_arguments.temp_dir
+
     if cli_arguments.do_glimmer:
         cromwell_inputs['ei_prediction.do_glimmer'] = 'true'
         if cli_arguments.do_glimmer is not True and os.access(cli_arguments.do_glimmer, os.R_OK):
@@ -103,7 +109,10 @@ def combine_arguments_prediction(cli_arguments):
         cromwell_inputs['ei_prediction.do_codingquarry'] = 'true'
         if cli_arguments.do_codingquarry is not True and os.access(cli_arguments.do_codingquarry, os.R_OK):
             cromwell_inputs['ei_prediction.codingquarry_training'] = cli_arguments.do_codingquarry
-
+
+    if cli_arguments.do_helixer:
+        cromwell_inputs['ei_prediction.do_helixer'] = 'true'
+
     if cli_arguments.no_augustus and cli_arguments.no_augustus is False:
         cromwell_inputs['ei_prediction.do_augustus'] = 'false'
 
@@ -222,8 +231,11 @@ def combine_arguments_prediction(cli_arguments):
         cromwell_inputs['ei_prediction.snap_extra_params'] = cli_arguments.snap_extra_params
     if cli_arguments.augustus_extra_params:
         cromwell_inputs['ei_prediction.augustus_extra_params'] = cli_arguments.augustus_extra_params
+    if cli_arguments.helixer_extra_params:
+        cromwell_inputs['ei_prediction.helixer_extra_params'] = cli_arguments.helixer_extra_params
     if cli_arguments.evm_extra_params:
         cromwell_inputs['ei_prediction.evm_extra_params'] = cli_arguments.evm_extra_params
+
 
     if cli_arguments.mikado_config:
         cromwell_inputs['ei_prediction.mikado_config'] = cli_arguments.mikado_config.name
@@ -246,7 +258,8 @@ def collect_prediction_output(run_metadata):
 
     if outputs['ei_prediction.glimmer']:
         symlink(outputs_path, outputs['ei_prediction.glimmer'])
-
+    if outputs['ei_prediction.helixer']:
+        symlink(outputs_path, outputs['ei_prediction.helixer'])
     if outputs['ei_prediction.snap']:
         symlink(outputs_path, outputs['ei_prediction.snap'])
     if outputs['ei_prediction.codingquarry']:
@@ -271,6 +284,7 @@ def collect_prediction_output(run_metadata):
     snap_prediction_path = os.path.join(predictions_path, "SNAP")
     codingquarry_prediction_path = os.path.join(predictions_path, "CodingQuarry")
     augustus_prediction_path = os.path.join(predictions_path, "Augustus")
+    helixer_prediction_path = os.path.join(predictions_path, "Helixer")
     if not os.path.exists(predictions_path):
         os.mkdir(predictions_path)
 
@@ -303,6 +317,14 @@ def collect_prediction_output(run_metadata):
     else:
         if os.path.exists(glimmer_prediction_path):
             shutil.rmtree(glimmer_prediction_path)
+
+    if outputs['ei_prediction.predictions_helixer']:
+        if not os.path.exists(helixer_prediction_path):
+            os.mkdir(helixer_prediction_path)
+        symlink(helixer_prediction_path, outputs['ei_prediction.predictions_helixer'])
+    else:
+        if os.path.exists(helixer_prediction_path):
+            shutil.rmtree(helixer_prediction_path)
 
     if outputs['ei_prediction.predictions_augustus']:
         if not os.path.exists(augustus_prediction_path):

annotation/prediction_module/main.wdl

@@ -15,7 +15,10 @@ workflow ei_prediction {
 		Boolean do_glimmer = false
 		Directory? glimmer_training
 		Boolean do_snap = false
+		Boolean do_helixer = false
 		File? snap_training
+		String? temp_dir
+
 		Boolean do_augustus = true
 		Array[File]? transcriptome_models  # Classify and divide into Gold, Silver and Bronze
 		Array[File]? homology_models  # Take as is
@@ -31,6 +34,8 @@ workflow ei_prediction {
 
 		File? repeats_gff  # These are passed through to augustus
 		File? extra_training_models  # These models are taken as-is directly as results from the training model selection
+		File? helixer_model #model used for helixer gene model prediction
+
 
 		Int flank = 200
 		Int kfold = 8
@@ -51,7 +56,7 @@ workflow ei_prediction {
 		String? snap_extra_params
 		String? augustus_extra_params
 		String? evm_extra_params
-
+		String? helixer_extra_params
 		RuntimeAttr augustus_resources
 	}
 
@@ -262,6 +267,18 @@ workflow ei_prediction {
 	Boolean train_utr = select_first([train_utr_, false])
 	Int total_models = select_first([num_models, 0])
 
+	#Run helixer predictions if GPU is available
+	if (do_helixer) {
+		call Helixer {
+			input:
+			genome = def_reference_genome,
+			model = helixer_model,
+			temp_dir = temp_dir,
+			species = species,
+			extra_params = helixer_extra_params
+		}
+	}
+
 	# Generate CodingQuarry predictions
 	# Considers lowercase as masked by default
 	if (total_models > 1500 && do_codingquarry) {
@@ -421,6 +438,7 @@ workflow ei_prediction {
 		augustus_predictions = def_augustus_predictions,
 		snap_predictions = SNAP.predictions,
 		glimmer_predictions = GlimmerHMM.predictions,
+		helixer_predictions = Helixer.predictions,
 		codingquarry_predictions = CodingQuarry.predictions,
 		codingquarry_fresh_predictions = CodingQuarryFresh.predictions,
 		hq_protein_alignments = hq_protein.processed_gff,
@@ -514,6 +532,7 @@ workflow ei_prediction {
 		File? codingquarry = EVM.formatted_codingquarry_predictions
 		File? codingquarry_fresh = EVM.formatted_codingquarry_fresh_predictions
 		File? augustus_abinitio = EVM.formatted_augustus_abinitio_predictions
+		File? helixer = EVM.formatted_helixer_predictions
 		Array[File]? augustus = EVM.formatted_augustus_runs_predictions
 		File evm_predictions = CombineEVM.predictions
 		File mikado_loci = MikadoPick.loci
@@ -1157,6 +1176,56 @@ task GlimmerHMM {
 	>>>
 }
 
+
+task Helixer {
+	input {
+		IndexedReference genome
+		File model
+		Int sequence_length
+		String species
+		String temp_dir
+		RuntimeAttr? resources
+	}
+
+    RuntimeAttr default_attr = object {
+        constraints: "avx|avx2|sse4",
+        cpu_cores: 8,
+        mem_gb: 64,
+        max_retries: 1,
+        queue: "ei-a100,ei-gpu"
+    }
+
+    RuntimeAttr runtime_attr = select_first([resources, default_attr])
+
+    Int cpus = select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
+	Int gpus = select_first([runtime_attr.gpu, default_attr.gpu])
+
+    runtime {
+        cpu: cpus
+        memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GB"
+        constraints: select_first([runtime_attr.constraints, default_attr.constraints])
+        maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
+        queue: select_first([runtime_attr.queue, default_attr.queue])
+		gpu: gpus
+    }
+
+
+	output {
+		File predictions = "helixer.predictions.gff3"
+	}
+
+	command <<<
+		set -euxo pipefail
+		ln -s ~{genome.fasta}
+		Helixer.py --model-filepath \
+		--temporary-dir ~{temp_dir} \
+		--species ~{species} \
+		--fasta-path ~{genome.fasta} \
+		~{helixer_extra_params} \
+		--gff-output-path  helixer.predictions.gff3
+	>>>
+}
+
 task GenerateModelProteins {
 	input {
 		IndexedReference genome
@@ -1393,6 +1462,7 @@ task EVM {
 		File? augustus_abinitio
 		File? snap_predictions
 		File? glimmer_predictions
+		File? helixer_predictions
 		File? codingquarry_predictions
 		File? codingquarry_fresh_predictions
 		File? hq_protein_alignments
@@ -1426,13 +1496,15 @@ task EVM {
 		File? formatted_codingquarry_fresh_predictions = "codingquarry_fresh.predictions.gff"
 		File? formatted_augustus_abinitio_predictions = "augustus_abinitio.predictions.gff"
 		Array[File]? formatted_augustus_runs_predictions = glob("augustus_*.predictions.gff")
+		File? formatted_helixer_predictions = "helixer.predictions.gff"
 
 		File? formatted_snap_predictions_stats = "snap.predictions.stats"
 		File? formatted_glimmer_predictions_stats = "glimmer.predictions.stats"
 		File? formatted_codingquarry_predictions_stats = "codingquarry.predictions.stats"
 		File? formatted_codingquarry_fresh_predictions_stats = "codingquarry_fresh.predictions.stats"
 		File? formatted_augustus_abinitio_predictions_stats = "augustus_abinitio.predictions.stats"
 		Array[File]? formatted_augustus_runs_predictions_stats = glob("augustus_*.predictions.stats")
+		File? formatted_helixer_predictions_stats = "helixer.predictions.gff.stats"
 	}
 
 	command <<<
@@ -1487,6 +1559,11 @@ task EVM {
 			mikado util stats augustus_abinitio.predictions.gff augustus_abinitio.predictions.stats
 		fi
 
+		if [ "~{helixer_predictions}" != "" ]; then
+			cat ~{helixer_predictions} | gff_to_evm glimmer | tee helixer.predictions.gff >> predictions.gff
+			mikado util stats helixer.predictions.gff helixer.predictions.stats
+		fi
+
 		augustus_run=0
 		for i in ~{sep=" " augustus_predictions}; do
 			((augustus_run++))

cromwell_configuration/slurm.conf

@@ -73,6 +73,7 @@ backend {
         Int memory_mb = 8000
         String? constraints
         String? queue = "ei-medium"
+        Int? gpu
         """
 
         submit = """
@@ -84,6 +85,15 @@ backend {
             --mem ${memory_mb} \
             --wrap "/bin/bash
             ${script}"
+        elif [ "${queue}" == "ei-a100" || "${queue}" == "ei-gpu" ] #gpu specific nodes in the cluster
+        then
+          sbatch -J ${job_name} --constraint="${constraints}" -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} \
+        	-p "${queue}" \
+            ${"-c " + cpu} \
+            --mem ${memory_mb} \
+            --gres=gpu:"${gpu}"
+            --wrap "/bin/bash
+            ${script}"
         else
         	sbatch -J ${job_name} --constraint="${constraints}" -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} \
         	-p ${queue} \

reat.yml

@@ -32,3 +32,4 @@ dependencies:
   - codingquarry=2.0
   - augustus=3.4.0
   - evidencemodeler=1.1.1
+

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="reat",
-    version="0.6.1",
+    version="0.7.1",
     packages=find_packages(".", exclude=["tests"]),
     url="https://github.com/ei-corebioinformatics/reat",
     classifiers=[
@@ -19,8 +19,8 @@
         "Programming Language :: Python :: 3.8",
     ],
     license="MIT",
-    author="Luis Yanes, Gemy Kaithakottil",
-    author_email="luis.yanes@earlham.ac.uk, gemy.kaithakottil@earlham.ac.uk",
+    author="Luis Yanes, Gemy Kaithakottil, Mariano Olivera Fedi",
+    author_email="luis.yanes@earlham.ac.uk, gemy.kaithakottil@earlham.ac.uk, mariano.olivera-fedi@earlham.ac.uk",
     description="Robust Eukaryotic Annotation Toolkit",
     zip_safe=False,
     keywords="gene annotation WDL pipeline workflow cromwell transcriptome homology",

singularity/build_image.sh

@@ -1,5 +1,5 @@
 set -euxo
-version=0.6.1
+version=0.7.1
 rundir=$(dirname "$(realpath "$0")")
 cd "$(mktemp -d)"
 cp "${rundir}"/reat_singularity.def reat.def