The workflows now follow snakefmt formatting. How number of new lines…

… are applied are a bit inconsistent right now, but I have submitted an issue for this snakemake/snakefmt#93

src/Snakemake/workflow/Twist_DNA_workflow.smk

@@ -2,42 +2,56 @@
 include: "../rules/Fastq/demultiplex.smk"
 include: "../rules/Fastq/fix_fastq_DNA.smk"
 
-if config["programs"]["Trimming"] == "Cutadapt" :
+
+if config["programs"]["Trimming"] == "Cutadapt":
+
     include: "../rules/Fastq/Cutadapt_trimming.smk"
-elif config["programs"]["Trimming"] == "Fastp" :
+
+
+elif config["programs"]["Trimming"] == "Fastp":
+
     include: "../rules/Fastq/Fastp_trimming.smk"
-else :
+
+
+else:
+
     include: "../rules/Fastq/move_fastq.smk"
-#include: "../rules/CNV/ONCOCNV.smk"
-#include: "../rules/CNV/cnvkit.smk"
-#include: "../rules/QC/check_coverage.smk"
-#include: "../rules/VCF_fix/Collect_results_DNA.smk" #Change folder!
-#include: "../rules/Mutect2/Mutect2.smk"
 
-if config["programs"]["Duplicates"] == "fgbio" :
+
+# include: "../rules/CNV/ONCOCNV.smk"
+# include: "../rules/CNV/cnvkit.smk"
+# include: "../rules/QC/check_coverage.smk"
+# include: "../rules/VCF_fix/Collect_results_DNA.smk" #Change folder!
+# include: "../rules/Mutect2/Mutect2.smk"
+
+
+if config["programs"]["Duplicates"] == "fgbio":
+
     include: "../rules/Alignment/fgbio.smk"
-else :
-    if config["programs"]["markduplicate"] == "GPU" :
+
+
+else:
+    if config["programs"]["markduplicate"] == "GPU":
+
         include: "../rules/Alignment/GPU_alignment.smk"
-    else :
+
+
+    else:
+
         include: "../rules/Alignment/bwa-mem.smk"
-        include: "../rules/Alignment/MarkDuplicates.smk"
 
+        include: "../rules/Alignment/MarkDuplicates.smk"
 include: "../rules/SNV/freebayes.smk"
 include: "../rules/SNV/mutect2.smk"
 include: "../rules/SNV/vardict_T.smk"
 include: "../rules/SNV/varscan.smk"
-
 include: "../rules/VCF_fix/fix_AF_all_callers.smk"
 include: "../rules/VCF_fix/normalize.smk"
 include: "../rules/VCF_fix/recall.smk"
 include: "../rules/VCF_fix/VEP.smk"
-
 include: "../rules/MSI/msisensor2.smk"
-
 include: "../rules/DNA_fusion/gridss.smk"
-
 include: "../rules/QC/samtools-picard-stats.smk"
 include: "../rules/QC/multiqc.smk"
-#include: "../rules/QC/cartool.smk"
+# include: "../rules/QC/cartool.smk"
 include: "../rules/QC/fastqc.smk"

src/Snakemake/workflow/gms_somatic_workflow.smk

@@ -1,11 +1,13 @@
 units = pd.read_table(config["units"], index_col=["sample", "unit"], dtype=str)
 units.index = units.index.set_levels([i.astype(str) for i in units.index.levels])  # enforce str in index
 
+
 def fastq_files(wildcards):
     return [v[0] for k, v in units.loc[wildcards.sample].items()]
 
-fastp_trimming_input=lambda wildcards: fastq_files(wildcards)
 
-include: "../rules/Fastq/Fastp_trimming.smk"
+fastp_trimming_input = lambda wildcards: fastq_files(wildcards)
 
-include: "../rules/Alignment/bwa-mem.smk"
+
+include: "../rules/Fastq/Fastp_trimming.smk"
+include: "../rules/Alignment/bwa-mem.smk"