test on RNAseq, ATACseq, scRNAseq, clean code and fix cosmetics #11

config/config.yaml

@@ -1,4 +1,3 @@
-# always use absolute paths
 
 ##### RESOURCES #####
 # memory (mem) in MB
@@ -49,5 +48,4 @@ file_type: "pdf"
 # define custom colors (in HEX) for groups from the annotation file
 track_colors:
     untreated: "#800080"
-    LO28_2h: "#00FFFF"
-    LO28_6h: "#FF0000"
+    treated: "#00FFFF"

workflow/Snakefile

@@ -35,6 +35,7 @@ sc_groups = list(set(group for data in sc_file_group_dict.values() for group in
 
 # groups for actual visualization
 plot_groups = sc_groups + list(set([group for group in annot['group'] if not group.endswith('.tsv')]))
+plot_groups.sort()
 
 result_path = os.path.join(config["result_path"], module_name)
 

workflow/rules/common.smk

@@ -10,8 +10,8 @@ def get_bams(wildcards):
     else:
         return annot.loc[annot['group']==wildcards.group,'bam'].to_list()
 
-def get_bigWigs(wildcards):
-    return expand(os.path.join(result_path, 'bigWigs','{group}.bw'),group=plot_groups)
+# def get_bigWigs(wildcards):
+#     return expand(os.path.join(result_path, 'bigWigs','{group}.bw'),group=sort(plot_groups))
 
 def parse_gene(gene):
     count = 0

workflow/rules/prepare.smk

@@ -1,5 +1,7 @@
 # create BED file of genes/genomic regions
 rule make_bed:
+    input:
+        config["gene_list"],
     output:
         bed_file = os.path.join(result_path,'genes.bed'),
     resources:

workflow/rules/visualization.smk

@@ -52,10 +52,10 @@ rule ucsc_hub:
                 track = ['track {}'.format(group),
                          'shortLabel {}'.format(group),
                          'longLabel {}'.format(group),
-                         'bigDataUrl {}.bigWig'.format(group),
+                         'bigDataUrl {}.bw'.format(group),
                          'parent {} on'.format(config["project_name"]),
                          'type bigWig', 'windowingFunction mean',
-                         'color {}'.format(track_color),
+                         'color {}'.format(','.join(map(str, track_color))),
                          '', '']
 
                 track_db += track
@@ -66,7 +66,8 @@ rule ucsc_hub:
 # plot genome tracks of groups using pyGenomeTracks wrapper gtracks
 rule plot_tracks:
     input:
-        get_bigWigs,
+        bigWigs = expand(os.path.join(result_path, 'bigWigs','{group}.bw'), group=plot_groups),
+#         get_bigWigs,
     output:
         genome_track = report(os.path.join(result_path, 'tracks','{gene}.'+config["file_type"]), 
                               caption="../report/genome_tracks.rst", 
@@ -101,7 +102,7 @@ rule plot_tracks:
         export GTRACKS_GENES_PATH={params.genome_bed}
         
         gtracks {params.coordinates} \
-            {input} \
+            {input.bigWigs} \
             {output.genome_track} \
             --genes {params.genome_bed} \
             {params.ymax} \