Merge branch 'develop' into novaseq_x_validation

requirements.txt

@@ -1,9 +1,8 @@
 hydra-genetics==1.11.1
 pandas>=1.3.1
-pulp<2.8.0
+pulp<2.8
 snakemake==7.22.0
 singularity==3.0.0
-jinja2==3.0.1
 networkx
 drmaa
 cyvcf2==0.30.16

start_HG_marvin.sh

@@ -9,10 +9,6 @@ module load singularity/3.7.1
 
 poirotFolder=/beegfs-storage/projects/wp3/nobackup/TWIST/Bin/Poirot
 
-python3.9 -m venv ${poirotFolder}/hydra_env
-source ${poirotFolder}/hydra_env/bin/activate
-pip install -r ${poirotFolder}/requirements.txt
-
 fastqFolder=$1
 sequencerun=$2    #Sequence ID
 startDir=$PWD
@@ -38,6 +34,10 @@ rsync -ru ${poirotFolder}/config /scratch/wp3/TWIST/${sequencerun}/  && \
 
 cd /scratch/wp3/TWIST/${sequencerun}/  && \
 
+python3.9 -m venv hydra_env && \
+source hydra_env/bin/activate && \
+pip install -r ${poirotFolder}/requirements.txt && \
+
 # Create sample and unit files
 hydra-genetics create-input-files -d ${fastqFolder} -t N --tc 0 -f && \
 

workflow/rules/common.smk

@@ -238,16 +238,15 @@ def get_vcfs_for_svdb_merge(wildcards, input):
 def compile_output_list(wildcards):
     output_files = []
     types = set([unit.type for unit in units.itertuples()])
-    for output, values in output_json.items():
-        if values["name"] == "_copy_upd_regions_bed":
-            output_files += set(
-                [
-                    output.format(sample=sample, type=unit_type)
-                    for sample in samples[samples.trio_member == "proband"].index
-                    for unit_type in get_unit_types(units, sample)
-                    if unit_type in set(output_json[output]["types"]).intersection(types)
-                ]
-            )
+    for output in output_json:
+        if output == "results/{sample}/{sample}.upd_regions.bed":
+            for sample in samples[samples.trio_member == "proband"].index:
+                proband_trio_id = samples[samples.index == sample].trioid.iloc[0]
+                trio_num = samples[samples.trioid == proband_trio_id].shape[0]
+                if trio_num != 3:
+                    continue
+                else:
+                    output_files.append(output.format(sample=sample))
         else:
             output_files += set(
                 [