snakefmt

snakemake-workflows · Oct 20, 2023 · c576b56 · c576b56
1 parent 83241b9
commit c576b56
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -169,7 +169,7 @@ enrichment_env = render_enrichment_env()
 
 def kallisto_quant_input(wildcards):
     if is_3prime_experiment:
-        return "results/mane_3prime_reads/{sample}-{unit}.fastq",
+        return "results/mane_3prime_reads/{sample}-{unit}.fastq"
     elif not is_single_end(wildcards.sample, wildcards.unit):
         return expand(
             "results/trimmed/{{sample}}-{{unit}}.{group}.fastq.gz", group=[1, 2]

diff --git a/workflow/rules/quant_3prime.smk b/workflow/rules/quant_3prime.smk
@@ -47,7 +47,7 @@ rule get_only_mane_select_reads_closest_to_3_prime:
 
 rule get_mane_fastq:
     input:
-        bam="results/mapped_3prime_mane/{sample}-{unit}.mane_select_closest_to_3_prime.bam"
+        bam="results/mapped_3prime_mane/{sample}-{unit}.mane_select_closest_to_3_prime.bam",
     output:
         fastq="results/mane_3prime_reads/{sample}-{unit}.fastq",
     log:
@@ -111,4 +111,4 @@ rule kallisto_samtools_index:
         extra="",  # optional params string
     threads: 4  # This value - 1 will be sent to -@
     wrapper:
-        "v1.18.3/bio/samtools/index"
+        "v1.18.3/bio/samtools/index"
diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -32,7 +32,11 @@ rule get_annotation:
 
 rule get_transcript_info:
     output:
-        multiext("resources/transcripts_annotation", ".results.rds", ".mane_strand_length.tsv"),
+        multiext(
+            "resources/transcripts_annotation",
+            ".results.rds",
+            ".mane_strand_length.tsv",
+        ),
     params:
         species=get_bioc_species_name(),
         version=config["resources"]["ref"]["release"],

diff --git a/workflow/rules/ref_3prime.smk b/workflow/rules/ref_3prime.smk
@@ -10,6 +10,7 @@ rule cds_polyA_T_removal:
     script:
         "../scripts/remove_poly_tails.py"
 
+
 rule get_mane_transcripts_fasta:
     input:
         fasta="resources/transcriptome.cdna.without_poly_a.fasta",