diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf index fa61ab6b06c7a0d554d644d7dede715c641e1bce..5997fdf137047b6b2c98159e810dc6259d948980 100644 --- a/src/nf_modules/fastp/main.nf +++ b/src/nf_modules/fastp/main.nf @@ -46,30 +46,30 @@ process fastp_default { if (reads instanceof List) """ fastp --thread ${task.cpus} \ ---qualified_quality_phred 20 \ ---disable_length_filtering \ ---detect_adapter_for_pe \ -${params.fastp} \ ---in1 ${reads[0]} \ ---in2 ${reads[1]} \ ---out1 ${pair_id}_R1_trim.fastq.gz \ ---out2 ${pair_id}_R2_trim.fastq.gz \ ---html ${pair_id}.html \ ---json ${pair_id}_fastp.json \ ---report_title ${pair_id} + --qualified_quality_phred 20 \ + --disable_length_filtering \ + --detect_adapter_for_pe \ + ${params.fastp} \ + --in1 ${reads[0]} \ + --in2 ${reads[1]} \ + --out1 ${pair_id}_R1_trim.fastq.gz \ + --out2 ${pair_id}_R2_trim.fastq.gz \ + --html ${pair_id}.html \ + --json ${pair_id}_fastp.json \ + --report_title ${pair_id} """ else """ fastp --thread ${task.cpus} \ ---qualified_quality_phred 20 \ ---disable_length_filtering \ ---detect_adapter_for_pe \ -${params.fastp} \ ---in1 ${reads} \ ---out1 ${pair_id}_trim.fastq.gz \ ---html ${pair_id}.html \ ---json ${pair_id}_fastp.json \ ---report_title ${pair_id} + --qualified_quality_phred 20 \ + --disable_length_filtering \ + --detect_adapter_for_pe \ + ${params.fastp} \ + --in1 ${reads} \ + --out1 ${pair_id}_trim.fastq.gz \ + --html ${pair_id}.html \ + --json ${pair_id}_fastp.json \ + --report_title ${pair_id} """ } @@ -91,47 +91,45 @@ process fastp_accel_1splus { if (reads instanceof List) """ fastp --thread ${task.cpus} \ ---disable_quality_filtering \ ---disable_length_filtering \ ---disable_trim_poly_g \ ---stdout \ ---in1 ${reads[0]} \ ---in2 ${reads[1]} \ ---out1 ${pair_id}_R1_trim.fastq.gz \ ---out2 ${pair_id}_R2_trim.fastq.gz | \ -fastp --thread ${task.cpus} \ ---stdin \ ---trim_front1=10 \ ---trim_tail1=10 \ ---trim_tail2=10 \ ---qualified_quality_phred 20 \ ---disable_length_filtering \ ---detect_adapter_for_pe \ -${params.fastp} \ ---html ${pair_id}.html \ ---json ${pair_id}_fastp.json \ ---report_title ${pair_id} + --disable_quality_filtering \ + --disable_length_filtering \ + --disable_trim_poly_g \ + --stdout \ + --in1 ${reads[0]} \ + --in2 ${reads[1]} \ + --out1 ${pair_id}_R1_trim.fastq.gz \ + --out2 ${pair_id}_R2_trim.fastq.gz | \ + fastp --thread ${task.cpus} \ + --stdin \ + --trim_front1=10 \ + --trim_front2=10 \ + --qualified_quality_phred 20 \ + --disable_length_filtering \ + --detect_adapter_for_pe \ + ${params.fastp} \ + --html ${pair_id}.html \ + --json ${pair_id}_fastp.json \ + --report_title ${pair_id} """ else """ fastp --thread ${task.cpus} \ ---disable_quality_filtering \ ---disable_length_filtering \ ---disable_trim_poly_g \ ---stdout \ ---in1 ${reads[0]} \ ---out1 ${pair_id}_R1_trim.fastq.gz \ -fastp --thread ${task.cpus} \ ---stdin \ ---trim_front1=10 \ ---trim_tail1=10 \ ---qualified_quality_phred 20 \ ---disable_length_filtering \ ---detect_adapter_for_pe \ -${params.fastp} \ ---html ${pair_id}.html \ ---json ${pair_id}_fastp.json \ ---report_title ${pair_id} + --disable_quality_filtering \ + --disable_length_filtering \ + --disable_trim_poly_g \ + --stdout \ + --in1 ${reads[0]} \ + --out1 ${pair_id}_R1_trim.fastq.gz \ + fastp --thread ${task.cpus} \ + --stdin \ + --trim_front1=10 \ + --qualified_quality_phred 20 \ + --disable_length_filtering \ + --detect_adapter_for_pe \ + ${params.fastp} \ + --html ${pair_id}.html \ + --json ${pair_id}_fastp.json \ + --report_title ${pair_id} """ }