fix analysis after contamination removal

snakemodules/analysis.smk

@@ -52,9 +52,9 @@ if config["SICKLE"]=="no":
     if config["remove_contamination"]=="yes":
         rule email_unmapped_analysis_no_filtler_after_clean:
             input:
-                single=expand("{p}/{s}/single.fastq", p=WORK_DIR, s=SAMPLES),
-                paired1=expand("{p}/{s}/paired.1.fastq", p=WORK_DIR, s=SAMPLES),
-                paired2=expand("{p}/{s}/paired.2.fastq", p=WORK_DIR, s=SAMPLES)
+                single=expand("{p}/{s}/single_clean.fastq", p=WORK_DIR, s=SAMPLES),
+                paired1=expand("{p}/{s}/paired_1_clean.fastq", p=WORK_DIR, s=SAMPLES),
+                paired2=expand("{p}/{s}/paired_2_clean.fastq", p=WORK_DIR, s=SAMPLES)
             output:
                 notify_file=temp("notify/unmapped_analysis_no_filtler_after_clean.txt")
             params:
@@ -78,9 +78,9 @@ if config["SICKLE"]=="no":
         rule unmapped_analysis_no_filtler_after_clean:
             input:
                 notify="notify/unmapped_analysis_no_filtler_after_clean.txt",
-                single=expand("{p}/{s}/single.fastq", p=WORK_DIR, s=SAMPLES),
-                paired1=expand("{p}/{s}/paired.1.fastq", p=WORK_DIR, s=SAMPLES),
-                paired2=expand("{p}/{s}/paired.2.fastq", p=WORK_DIR, s=SAMPLES)
+                single=expand("{p}/{s}/single_clean.fastq", p=WORK_DIR, s=SAMPLES),
+                paired1=expand("{p}/{s}/paired_1_clean.fastq", p=WORK_DIR, s=SAMPLES),
+                paired2=expand("{p}/{s}/paired_2_clean.fastq", p=WORK_DIR, s=SAMPLES)
             output:
                 RESULTS_DIR + "/read_numbers_no_sickle_after_clean.png"
             conda: