fixed linting issues

Author: niekwit

workflow/rules/damid.smk

@@ -2,9 +2,9 @@ rule damidseq_pipeline: # ignore dir wildcard in expand statement (double braces
     input:
         git="resources/damidseq_pipeline",
         flag=expand("results/trimmed/{dir}/{sample}.flag", dir=DIRS, sample=SAMPLES),
-        gatc=f"resources/{resources.genome}.GATC.gff",
+        gatc=f"resources/genome.GATC.gff",
         idx=multiext(
-            f"resources/bowtie2_index/{resources.genome}/index",
+            f"resources/bowtie2_index/index",
             ".1.bt2",
             ".2.bt2",
             ".3.bt2",
@@ -13,7 +13,7 @@ rule damidseq_pipeline: # ignore dir wildcard in expand statement (double braces
             ".rev.2.bt2",
         ),
     params:
-        idxdir=f"resources/bowtie2_index/{resources.genome}/index",
+        idxdir=f"resources/bowtie2_index/index",
         paired=paired_end(),
         extra=config["extra"],
     output:

workflow/rules/resources.smk

@@ -40,6 +40,8 @@ rule chrom_sizes:
     threads: config["resources"]["plotting"]["cpu"]
     resources: 
         runtime=config["resources"]["plotting"]["time"]
+    conda:
+        "../envs/damid.yaml"
     shell:
         "awk '{{print $1,$2}}' {input.fai} | "
         r"sed 's/ /\t/'  > {output}"

workflow/rules/setup.smk

@@ -3,16 +3,16 @@ rule make_gatc_tracks:
         sw="resources/damidseq_pipeline",
         fa=resources.fasta,
     output:
-        gatc=f"resources/{resources.genome}.GATC.gff",
+        gatc=f"resources/genome.GATC.gff",
     params:
-        genome=f"resources/{resources.genome}",
+        genome=f"resources/genome",
     threads: config["resources"]["fastqc"]["cpu"],
     resources:
         time=config["resources"]["fastqc"]["time"],
     conda:
         "../envs/damid.yaml",
     log:
-        f"logs/make_gatc_tracks/{resources.genome}.log",
+        f"logs/make_gatc_tracks/tracks.log",
     shell:
         "perl resources/damidseq_pipeline/gatc.track.maker.pl "
         "--name={params.genome} "
@@ -24,7 +24,7 @@ rule bowtie2_build_index:
         ref=resources.fasta,
     output:
         multiext(
-            f"resources/bowtie2_index/{resources.genome}/index",
+            f"resources/bowtie2_index/index",
             ".1.bt2",
             ".2.bt2",
             ".3.bt2",

workflow/scripts/average_bigwig.py

@@ -1,11 +1,13 @@
+#DELETE THIS SCRIPT LATER
+
 from snakemake.shell import shell
 
 # Load Snakemake variables
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 threads = snakemake.threads
 
 all_bw = snakemake.input
-sample = snakemake.wildcards["sample"]
+sample = snakemake.wildcards["bg_sample"]
 out = snakemake.output["bw"]
 
 # Get all samples in condition

workflow/scripts/general_functions.smk

@@ -38,7 +38,7 @@ def samples(bedgraph=False):
                     not_found.append(r1)
     if len(not_found) != 0:
         not_found = "\n".join(not_found)
-        raise ValueError(f"ERROR: following files not found:\n{not_found}")
+        raise ValueError(f"following files not found:\n{not_found}")
 
     # Only return non-Dam samples if bedgraph is True
     if bedgraph: