fastp: add nf modules files

src/nf_modules/fastp/fastp_paired.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastp_fastq {
+        container = "fastp:0.19.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastp_fastq {
+        cpus = 1
+        container = "file://bin/fastp:0.19.7.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastp_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastp/0.19.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}

src/nf_modules/fastp/fastp_paired.nf

+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process fastp_fastq {
+  tag "$pair_id"
+  publishDir "results/fastq/fastp/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+    file "*.{zip,html}" into fastp_report
+    set pair_id, file "*.fastq.gz" fastq_trim_files
+
+  script:
+"""
+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 \
+--report_title ${pair_id}
+"""
+}

src/nf_modules/fastp/fastp_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fastp_fastq {
+        container = "fastp:0.19.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastp_fastq {
+        cpus = 1
+        container = "file://bin/fastp:0.19.7.sif"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fastp_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "fastp/0.19.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}

src/nf_modules/fastp/fastp_single.nf

+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { fastq_files }
+
+process fastp_fastq {
+  tag "$file_id"
+  publishDir "results/fastq/fastp/", mode: 'copy'
+
+  input:
+  set file_id, file(reads) from fastq_files
+
+  output:
+    file "*.{zip,html}" into fastp_report
+    set file_id, file "*.fastq.gz" fastq_trim_files
+
+  script:
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--in1 ${reads} \
+--out1 ${file_id}_R1_trim.fastq.gz \
+--html ${file_id}.html \
+--report_title ${file_id}
+"""
+}

src/nf_modules/fastp/tests.sh

+./nextflow src/nf_modules/fastp/fastp_paired.nf \
+  -c src/nf_modules/fastp/fastp_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastp/fastp_single.nf \
+  -c src/nf_modules/fastp/fastp_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/fastp/fastp_paired.nf \
+  -c src/nf_modules/fastp/fastp_paired.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastp/fastp_single.nf \
+  -c src/nf_modules/fastp/fastp_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi