Format

tdayris · Jul 10, 2024 · 7ebc870 · 7ebc870
1 parent 884135a
commit 7ebc870
Showing 1 changed file with 24 additions and 44 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -173,10 +173,8 @@ def lookup_genomes(
     """
     Run lookup function with default parameters in order to search user-provided sequence/annotation files
     """
-    query: str = (
-        "species == '{wildcards.species}' & build == '{wildcards.build}' & release == '{wildcards.release}'".format(
-            wildcards=wildcards
-        )
+    query: str ="species == '{wildcards.species}' & build == '{wildcards.build}' & release == '{wildcards.release}'".format(
+        wildcards=wildcards
     )
 
     query_result: str | float = getattr(
@@ -194,10 +192,8 @@ def get_dna_fasta(
     """
     Return path to the final DNA fasta sequences
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="dna_fasta", default=default, genomes=genomes)
 
@@ -208,10 +204,8 @@ def get_cdna_fasta(
     """
     Return path to the final cDNA fasta sequences
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="cdna_fasta", default=default, genomes=genomes)
 
@@ -222,10 +216,8 @@ def get_transcripts_fasta(
     """
     Return path to the final cDNA transcripts fasta sequences
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.transcripts.fasta".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.transcripts.fasta".format(
+        wildcards=wildcards
     )
     return lookup_genomes(
         wildcards, key="transcripts_fasta", default=default, genomes=genomes
@@ -254,10 +246,8 @@ def get_dna_fai(
     """
     Return path to the final DNA fasta sequences index
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta.fai".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta.fai".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="dna_fai", default=default, genomes=genomes)
 
@@ -268,10 +258,8 @@ def get_cdna_fai(
     """
     Return path to the final cDNA fasta sequences index
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta.fai".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta.fai".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="cdna_fai", default=default, genomes=genomes)
 
@@ -282,10 +270,8 @@ def get_transcripts_fai(
     """
     Return path to the final cDNA transcripts fasta sequences index
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.transcripts.fasta.fai".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.transcripts.fasta.fai".format(
+        wildcards=wildcards
     )
     return lookup_genomes(
         wildcards, key="transcripts_fai", default=default, genomes=genomes
@@ -314,10 +300,8 @@ def get_gtf(
     """
     Return path to the final genome annotation (GTF formatted)
     """
-    default: str = (
-        "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.gtf".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.gtf".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="gtf", default=default, genomes=genomes)
 
@@ -328,10 +312,8 @@ def get_gff(
     """
     Return path to the final genome annotation (GFF3 formatted)
     """
-    default: str = (
-        "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.gff3".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.gff3".format(
+        wildcards=wildcards
     )
     return lookup_genomes(wildcards, key="gff3", default=default, genomes=genomes)
 
@@ -432,10 +414,8 @@ def get_genepred_bed(
     """
     Return path to bed-formatted genepred file
     """
-    default: str = (
-        "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.genePred.bed".format(
-            wildcards=wildcards
-        )
+    default: str = "reference/annotation/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.genePred.bed".format(
+        wildcards=wildcards
     )
     return lookup_genomes(
         wildcards,
@@ -462,10 +442,10 @@ def get_fair_bowtie2_mapping_target(
     Dictionnary of expected output files
     """
     # Include requirements of previous pipelines
-    fair_genome_indexer_targets: dict[str, list[str] | str] = (
-        fair_genome_indexer.get_fair_genome_indexer_target(
-            wildcards=wildcards, genomes=genomes, samples=samples
-        )
+    fair_genome_indexer_targets: dict[
+        str, list[str] | str
+    ] = fair_genome_indexer.get_fair_genome_indexer_target(
+        wildcards=wildcards, genomes=genomes, samples=samples
     )
 
     fair_fastqc_multiqc_targets: dict[str, list[str]] = dict(