add fix for processing when reads become too small

DennisSchmitz · Feb 22, 2021 · d8192a9 · d8192a9
1 parent 55ccd93
commit d8192a9
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/bin/rules/Nano_Ref_Cut-primers.smk b/bin/rules/Nano_Ref_Cut-primers.smk
@@ -14,4 +14,5 @@ rule Cut_primers:
     shell:
         """
 python bin/scripts/RemoveONTPrimers.py --input {input.fastq} --reference {input.ref} --primers {input.primers} --threads {threads} --output {output}
+sed -i "N;N;N;/\\n\\n/d" {output}
         """
diff --git a/config/pipeline_parameters.yaml b/config/pipeline_parameters.yaml
@@ -31,7 +31,7 @@ threads:
     Nanopore_reference_alignment: 6
     Nanopore_SoftClipper: 2
     Nanopore_cleanup: 4
-    Nanopore_primer_removal: 26
+    Nanopore_primer_removal: 12
     Nanopore_QC: 6
 
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