From 7ebc870e9ee03354aba5784236e836dfc4f060a2 Mon Sep 17 00:00:00 2001 From: tdayris Date: Wed, 10 Jul 2024 09:33:04 +0200 Subject: [PATCH] Format --- workflow/rules/common.smk | 68 ++++++++++++++------------------------- 1 file changed, 24 insertions(+), 44 deletions(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 186fe79..ceebed3 100644 --- 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(