Fix source functions and errors.

Ribo-seq/Ribo-seq.snakefile

@@ -134,7 +134,7 @@ from libdeseq import do_deseq2
 from libhts import status_setter
 from libhts import median_ratio_to_pseudo_ref_size_factors, size_factor_correlations
 from libhts import plot_paired_scatters, plot_norm_correlations, plot_counts_distribution, plot_boxplots, plot_histo
-from libworkflows import texscape, ensure_relative, cleanup_and_backup
+from libworkflows import texscape, wc_applied, ensure_relative, cleanup_and_backup
 from libworkflows import get_chrom_sizes, column_converter, make_id_list_getter
 from libworkflows import read_int_from_file, strip_split, file_len, last_lines, save_plot, SHELL_FUNCTIONS
 from libworkflows import sum_by_family, read_feature_counts, sum_feature_counts, sum_htseq_counts, warn_context
@@ -194,7 +194,7 @@ EFF_LIBS = list(config["transcriptome_TPM"].keys())
 series_dict = config["series"]
 SERIES_TYPES = list(series_dict.keys())
 genotype_series = series_dict["genotype_series"]
-dt_series = series_dict["dt_series"]
+dt_series = series_dict.get("dt_series", {})
 merged_series = merge_with(concat_lists, *series_dict.values())
 ALL_SERIES = list(merged_series.keys())
 #all_libs_in series = concat_lists(merge_with(concat_lists, *series_dict.values()).values())
@@ -711,6 +711,7 @@ rule select_size_range:
         """
 
 
+@wc_applied
 def source_fastq(wildcards):
     """Determine the fastq file corresponding to a given read type."""
     read_type = wildcards.read_type
@@ -940,6 +941,7 @@ rule count_RPF:
             nb_RPF_file.write(f"{nb_RPF}\n")
         
 
+@wc_applied
 def source_counts(wildcards):
     """Determines from which rule the gathered counts should be sourced."""
     if wildcards.biotype == "alltypes":
@@ -1737,6 +1739,7 @@ def bamcoverage_filter(wildcards):
         return ""
 
 
+@wc_applied
 def source_norm_file(wildcards):
     return rules.make_read_counts_summary.output.summary
 
@@ -2840,7 +2843,7 @@ rule plot_size_distribution:
     input:
         rules.compute_size_distribution.output
     output:
-        OPJ("figures", "{lib}_{{rep}}", "{read_type}_size_distribution.pdf"),
+        OPJ("figures", "{lib}_{rep}", "{read_type}_size_distribution.pdf"),
     message:
         "Plotting size distribution for {wildcards.lib}_{wildcards.rep}_{wildcards.read_type}."
     run: