Correct index for R1-2/single for oldsamplename

metagenlab · Jul 6, 2020 · 892c3c2 · 892c3c2
1 parent 51641fd
commit 892c3c2
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/rules/0_preprocessing/QC_raw_reads.rules b/rules/0_preprocessing/QC_raw_reads.rules
@@ -56,7 +56,6 @@ def sample_list_overall_QC():
     for i in set(all_samples[config['run_column']]):
         samples =  list(all_samples.index.values[all_samples[config["run_column"]] == i])
         for s in samples:
-            print(reads_ext)
             suffix_s = reads_ext[s]
             combined_values = expand("QC/FastQC/raw_reads/{RUN}/{sample}_{suffix}_fastqc.zip", RUN = i, sample = s, suffix = suffix_s)
             file_list = file_list + combined_values

diff --git a/rules/0_preprocessing/get_reads.rules b/rules/0_preprocessing/get_reads.rules
@@ -91,14 +91,14 @@ if "local_samples" in config.keys():
             read_correct[sample] = reads_local[old_sample_name]
 
             if "LibraryLayout" in list(local_data):
-                if local_data.loc[i, "LibraryLayout"].lower()=="paired":
-                    reads_ext[i]=["R1", "R2"]
+                if local_data.loc[sample, "LibraryLayout"].lower()=="paired":
+                    reads_ext[sample]=["R1", "R2"]
                 elif sra_data.loc[i, "LibraryLayout"].lower()=="single":
-                    reads_ext[i]=["single"]
+                    reads_ext[sample]=["single"]
                 else:
                     raise ValueError("Problem in the sra file, LibraryLayout badly defined")
             else:
-                reads_ext[i]=["R1", "R2"]
+                reads_ext[sample]=["R1", "R2"]
 
     original_names = original_correct
     reads_local = read_correct