move qc_pe

Author: vmikk

modules/Illumina_pe.nf

@@ -125,57 +125,6 @@ process qc_se {
 }
 
 
-// Quality filtering for pair-end reads
-process qc_pe {
-
-    label "main_container"
-
-    // cpus 10
-
-    input:
-      path input_R1
-      path input_R2
-
-    output:
-      path "QC_R1.fq.gz", emit: filtered_R1
-      path "QC_R2.fq.gz", emit: filtered_R2
-
-    script:
-    filter_avgphred  = params.qc_avgphred  ? "--average_qual ${params.qc_avgphred}"                 : "--average_qual 0"
-    filter_phredmin  = params.qc_phredmin  ? "--qualified_quality_phred ${params.qc_phredmin}"      : ""
-    filter_phredperc = params.qc_phredperc ? "--unqualified_percent_limit ${params.qc_phredperc}"   : ""
-    filter_polyglen  = params.qc_polyglen  ? "--trim_poly_g --poly_g_min_len ${params.qc_polyglen}" : ""
-    """
-    echo -e "QC\\n"
-    echo -e "Input R1: " ${input_R1}
-    echo -e "Input R2: " ${input_R2}
-
-    ## If `filter_phredmin` && `filter_phredperc` are specified,
-    # Filtering based on percentage of unqualified bases
-    # how many percents of bases are allowed to be unqualified (Q < 24)
-        
-    fastp \
-      --in1 ${input_R1} \
-      --in2 ${input_R2} \
-      --disable_adapter_trimming \
-      --n_base_limit ${params.qc_maxn} \
-      ${filter_avgphred} \
-      ${filter_phredmin} \
-      ${filter_phredperc} \
-      ${filter_polyglen} \
-      --length_required 100 \
-      --thread ${task.cpus} \
-      --html qc.html \
-      --json qc.json \
-      --out1 QC_R1.fq.gz \
-      --out2 QC_R2.fq.gz
-
-    echo -e "\\nQC finished"
-    """
-}
-
-
-
 // Validate tags for demultiplexing
 process tag_validation {