5' trimming option for fastp optional (to be used only with Arima Hi-…

…C library prep kit generated data)

workflow/rules/fastp.smk

@@ -12,6 +12,10 @@ rule fastp:
         reverse_out="results/fastp/hic_trim_2.fastq.gz",
         json="results/fastp/hic_report_fastp.HiC.json",
         html="results/fastp/hic_report_fastp.HiC.html",
+    params:
+        optional_params=" ".join(
+            f"{k} {v}" for k, v in config["fastp"]["optional_params"].items() if v
+        ),
     threads: config["medium"]["t"]
     log:
         "logs/fastp.log",
@@ -21,5 +25,5 @@ rule fastp:
         "../envs/fastp.yaml"
     shell:
         """
-        fastp -p -i {input.forward_in} -I {input.reverse_in} -o {output.forward_out} -O {output.reverse_out} --cut_front --cut_front_window_size 5  --detect_adapter_for_pe --json {output.json} --html {output.html} --thread {threads} >> {log} 2>&1
+        fastp -p -i {input.forward_in} -I {input.reverse_in} -o {output.forward_out} -O {output.reverse_out} --detect_adapter_for_pe --json {output.json} --html {output.html} --thread {threads} {params.optional_params} >> {log} 2>&1
         """