Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepr…

…ipe-batch

deeprvat/annotations/annotations.py

@@ -480,8 +480,8 @@ def deepripe_score_variant_onlyseq_all(
             pred = model.predict_on_batch(cropped_seqs)
             wild_indices = tf.range(pred.shape[0], delta=2)
             mut_indices = tf.range(1, pred.shape[0], delta=2)
-            pred_wild = pred[wild_indices]
-            pred_mut = pred[mut_indices]
+            pred_wild = pred[wild_indices, :]
+            pred_mut = pred[mut_indices, :]
             score = pred_mut - pred_wild
             avg_score += score
         predictions[choice] = avg_score / 4

deeprvat/annotations/setup_annotation_workflow.sh

@@ -9,7 +9,7 @@ echo "- vep"
 mkdir -p $REPO_DIR/ensembl-vep
 git clone https://github.com/Ensembl/ensembl-vep.git $REPO_DIR/ensembl-vep 
 cd $REPO_DIR/ensembl-vep
-git checkout release/109
+git checkout release/111
 perl INSTALL.pl --AUTO acfp --ASSEMBLY GRCh38 --CACHEDIR $VEP_CACHEDIR --PLUGINS CADD, SpliceAI, PrimateAI --PLUGINSDIR $VEP_PLUGINDIR --species homo_sapiens
 cd ../..
 

pipelines/annotations.snakefile

@@ -26,11 +26,12 @@ saved_deepripe_models_path = (
 )
 merge_nthreads = int(config.get("merge_nthreads") or 64)
 
-# init modules
-load_bfc = " ".join([config["bcftools_load_cmd"], "&&"])
-load_hts = " ".join([config["htslib_load_cmd"], "&&"])
-load_perl = " ".join([config["perl_load_cmd"], "&&"])
-load_vep = " ".join([config["vep_load_cmd"], "&&"])
+# If modules are used we load them here
+load_bfc = " ".join([config["bcftools_load_cmd"], "&&" if config["bcftools_load_cmd"] else ""])
+load_hts = " ".join([config["htslib_load_cmd"], "&&" if config["htslib_load_cmd"] else ""])
+load_perl = " ".join([config["perl_load_cmd"], "&&" if config["perl_load_cmd"] else ""])
+load_vep = " ".join([config["vep_load_cmd"], "&&" if config["vep_load_cmd"] else ""])
+
 
 # init data path
 vcf_pattern = config["vcf_file_pattern"]