fastp: update fastp to match CONTRIBUTING.md

src/nf_modules/fastp/main.nf

@@ -2,10 +2,9 @@ version = "0.20.1"
 container_url = "lbmc/fastp:${version}"
 
 params.fastp_protocol = ""
-params.fastp = ""
-params.fastp_pairedend = ""
-params.fastp_singleend = ""
 
+params.fastp = ""
+params.fastp_out = ""
 workflow fastp {
   take:
     fastq
@@ -31,165 +30,120 @@ workflow fastp {
 process fastp_default {
   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 \
-  ${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 ${pair_id}
-"""
-}
-
-process fastp_accel_1splus {
-  container = "${container_url}"
-  label "big_mem_multi_cpus"
-  tag "$pair_id"
-  publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
+  tag "$file_prefix"
+  if (params.fastp_out != "") {
+    publishDir "results/${params.fastp_out}", mode: 'copy'
+  }
 
   input:
-  tuple val(pair_id), path(reads)
+  tuple val(file_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
+    tuple val(file_id), path("*.fastq.gz"), emit: fastq
+    tuple val(file_id), path("*.html"), emit: html
+    tuple val(file_id), path("*.json"), emit: report
 
   script:
-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 | \
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  if (reads.size() == 2)
+  """
   fastp --thread ${task.cpus} \
-    --stdin \
-    --interleaved_in \
-    --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 \
+    --in1 ${reads[0]} \
+    --in2 ${reads[1]} \
+    --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}
+  """
+  else if (reads.size() == 1)
+  """
   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}
-"""
+    --in1 ${reads[0]} \
+    --out1 ${file_prefix}_trim.fastq.gz \
+    --html ${file_prefix}.html \
+    --json ${file_prefix}_fastp.json \
+    --report_title ${file_prefix}
+  """
 }
 
-process fastp_pairedend {
+process fastp_accel_1splus {
   container = "${container_url}"
   label "big_mem_multi_cpus"
-  tag "$pair_id"
-  publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
+  tag "$file_prefix"
+  if (params.fastp_out != "") {
+    publishDir "results/${params.fastp_out}", mode: 'copy'
+  }
 
   input:
-  tuple val(pair_id), path(reads)
+  tuple val(file_prefix), 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
+    tuple val(file_prefix), path("*.fastq.gz"), emit: fastq
+    tuple val(file_prefix), path("*.html"), emit: html
+    tuple val(file_prefix), path("*.json"), emit: report
 
   script:
-"""
-fastp --thread ${task.cpus} \
---qualified_quality_phred 20 \
---disable_length_filtering \
---detect_adapter_for_pe \
-${params.fastp_pairedend} \
---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 ${pair_id}
-"""
-}
-
-process fastp_singleend {
-  container = "${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
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
 
-  script:
-"""
-fastp --thread ${task.cpus} \
---qualified_quality_phred 20 \
---disable_length_filtering \
---detect_adapter_for_pe \
-${params.fastp_singleend} \
---in1 ${reads} \
---out1 ${pair_id}_trim.fastq.gz \
---html ${pair_id}.html \
---json ${pair_id}_fastp.json \
---report_title ${pair_id}
-"""
+  if (reads.size() == 2)
+  """
+  fastp --thread ${task.cpus} \
+    --disable_quality_filtering \
+    --disable_length_filtering \
+    --disable_trim_poly_g \
+    --stdout \
+    --in1 ${reads[0]} \
+    --in2 ${reads[1]} \
+    --out1 ${file_prefix}_R1_trim.fastq.gz \
+    --out2 ${file_prefix}_R2_trim.fastq.gz | \
+    fastp --thread ${task.cpus} \
+      --stdin \
+      --interleaved_in \
+      --trim_front1=10 \
+      --trim_front2=10 \
+      --qualified_quality_phred 20 \
+      --disable_length_filtering \
+      --detect_adapter_for_pe \
+      ${params.fastp} \
+      --html ${file_prefix}.html \
+      --json ${file_prefix}_fastp.json \
+      --report_title ${file_prefix}
+  """
+  else if (reads.size() == 1)
+  """
+  fastp --thread ${task.cpus} \
+    --disable_quality_filtering \
+    --disable_length_filtering \
+    --disable_trim_poly_g \
+    --stdout \
+    --in1 ${reads[0]} \
+    --out1 ${file_prefix}_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 ${file_prefix}.html \
+      --json ${file_prefix}_fastp.json \
+      --report_title ${file_prefix}
+  """
 }