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Verified Commit 8e1543d2 authored by Laurent Modolo's avatar Laurent Modolo
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fastp: fix accel_s1plus protocol

parent a7b03ba6
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......@@ -111,18 +111,19 @@ process fastp_accel_1splus {
--detect_adapter_for_pe \
--stdout \
--in1 ${reads[0]} \
--in2 ${reads[1]} \
--out1 ${file_prefix}_R1_trim.fastq.gz \
--out2 ${file_prefix}_R2_trim.fastq.gz | \
--in2 ${reads[1]} 2> /dev/null | \
fastp --thread ${task.cpus} \
--stdin \
--interleaved_in \
--trim_front1=10 \
--trim_front2=10 \
--disable_adapter_trimming \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
${params.fastp} \
--out1 ${file_prefix}_R1_trim.fastq.gz \
--out2 ${file_prefix}_R2_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
......@@ -135,15 +136,16 @@ process fastp_accel_1splus {
--disable_trim_poly_g \
--detect_adapter_for_pe \
--stdout \
--in1 ${reads[0]} \
--out1 ${file_prefix}_R1_trim.fastq.gz \
--in1 ${reads[0]} 2> /dev/null | \
fastp --thread ${task.cpus} \
--disable_adapter_trimming \
--stdin \
--trim_front1=10 \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
${params.fastp} \
--out1 ${file_prefix}_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
......
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