[fix](Aggregation): Namespace error fixed

Author: tdayris

rules/common.smk

@@ -180,9 +180,13 @@ def fq_pairs_w(wildcards) -> Dict[str, str]:
     """
     Dynamic wildcards call for snakemake.
     """
-    return {"fastq": fq_pairs_dict[wildcards.sample],
-            "gtf": refs_pack_dict["gtf"],
-            "index": "kallisto_index/genome_index"}
+    try:
+        return {"fastq": fq_pairs_dict[wildcards.sample],
+                "gtf": refs_pack_dict["gtf"],
+                "index": "kallisto_index/genome_index"}
+    except KeyError:
+        return {"fastq": fq_pairs_dict[wildcards.sample],
+                "index": "kallisto_index/genome_index"}
 
 
 def sample_id() -> List[str]:

scripts/aggregate_samples.py

@@ -59,7 +59,7 @@ def extract_field(*paths: List[str],
 
 
 if __name__ == '__main__':
-    makedirs(os.path.dirname(snakemake.output["est_counts"]))
+    makedirs(op.dirname(snakemake.output["est_counts"]))
 
     for column in ["est_counts", "tpm"]:
         data = extract_field(

tests/config.yaml

@@ -5,7 +5,7 @@ params:
   kallisto_index_extra: \-\-kmer-size=5
   kallisto_quant_extra: ''
 ref:
-  fasta: genomes/transcriptome.fasta
+  fasta: genome/transcriptome.fasta
   gtf: null
 singularity_docker_image: docker://continuumio/miniconda3:4.4.10
 threads: 1