snakefmt

tdayris · Jul 9, 2024 · 5e98698 · 5e98698
1 parent 256fc03
commit 5e98698
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Showing 2 changed files with 39 additions and 21 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -177,8 +177,10 @@ 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(
@@ -196,8 +198,10 @@ 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)
 
@@ -208,8 +212,10 @@ 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)
 
@@ -220,8 +226,10 @@ 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
@@ -250,8 +258,10 @@ 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)
 
@@ -262,8 +272,10 @@ 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)
 
@@ -274,8 +286,10 @@ 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
@@ -304,8 +318,10 @@ 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)
 
@@ -316,8 +332,10 @@ 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)
 

diff --git a/workflow/rules/fastq_screen.smk b/workflow/rules/fastq_screen.smk
@@ -19,15 +19,15 @@ rule fair_fastqc_multiqc_fastq_screen_single_ended:
         "benchmark/fair_fastqc_multiqc_fastq_screen_single_ended/{sample}.tsv"
     params:
         subset=lookup_config(
-            dpath="params/fair_fastqc_multiqc_fastq_screen/subset",
+            dpath="params/fair_fastqc_multiqc_fastq_screen_subset",
             default=10000,
         ),
         aligner=lookup_config(
-            dpath="params/fair_fastqc_multiqc_fastq_screen/aligner",
+            dpath="params/fair_fastqc_multiqc_fastq_screen_aligner",
             default="bowtie2",
         ),
         fastq_screen_config=lookup_config(
-            dpath="params/fair_fastqc_multiqc_fastq_screen/fastq_screen_config",
+            dpath="params/fair_fastqc_multiqc_fastq_screen_config",
         ),
     wrapper:
         f"{snakemake_wrappers_prefix}/bio/fastq_screen"