fastp: test paired_end & single_end process

src/nf_modules/fastp/main.nf

 version = "0.20.1"
 container_url = "lbmc/fastp:${version}"
 
+process fastp {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+  publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
+
+  input:
+  tuple val(pair_id), path(reads)
+
+  output:
+    tuple val(pair_id), path("*.fastq.gz"), emit: fastq
+    tuple val(pair_id), path("*.html"), emit: html
+    tuple val(pair_id), path("*.json"), emit: report
+
+  script:
+if (reads instanceof List)
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+--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 \
+--in1 ${reads} \
+--out1 ${pair_id}_trim.fastq.gz \
+--html ${pair_id}.html \
+--json ${pair_id}_fastp.json \
+--report_title ${pair_id}
+"""
+}
 
 process fastp_pairedend {
   container = "${container_url}"