cutadapt: add tests and config

src/nf_modules/cutadapt/1.14/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=1.14
+ENV PACKAGES build-essential=12.4* \
+             python3-pip=9.0.1* \
+             python3-setuptools=39.0.1* \
+             python3-dev=3.6.5* \
+             python3-wheel=0.30.0*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}

src/nf_modules/cutadapt/1.14/docker_init.sh

+#!/bin/sh
+docker build src/nf_modules/cutadapt/1.14 -t 'cutadapt:1.14'

src/nf_modules/cutadapt/cutadapt.config

+profiles {
+  docker {
+    docker {
+      temp = 'auto'
+      enabled = true
+    }
+    process {
+      $adaptor_removal {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  sge {
+    process{
+      $adaptor_removal {
+        beforeScript = "module purge; module load cutadapt/1.14"
+      }
+    }
+  }
+}
+
+profiles {
+  docker {
+    process {
+      $trimming {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load cutadapt/1.14"
+      }
+    }
+  }
+}

src/nf_modules/cutadapt/cutadapt.nf

@@ -67,10 +67,6 @@ process adaptor_removal {
 
 /*                      quality trimming                                     */
 
-${this.params.cutadapt} -q ${this.params.quality_threshold},${this.params.quality_threshold} -o ${tagname}_trim_R1.fastq.gz -p ${tagname}_trim_R2.fastq.gz ${file[0]} ${file[1]} > ${tagname}_cutadapt_report.txt"
-
-${this.params.cutadapt} -q ${this.params.quality_threshold},${this.params.quality_threshold} -o ${tagname}_trim.fastq.gz ${file} > ${tagname}_cutadapt_report.txt
-
 /*
 * for paired-end data
 */

src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf

+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$pair_id"
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+  file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}
+

src/nf_modules/cutadapt/tests/adaptor_removal_single.nf

+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$reads.baseName"
+
+  input:
+  file reads from fastq_files
+
+  output:
+  file "*_cut.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
+  -o ${reads.baseName}_cut.fastq.gz \
+  ${reads} > ${reads.baseName}_report.txt
+  """
+}
+

src/nf_modules/cutadapt/tests/tests.sh

+nextflow src/nf_modules/cutadapt/test/adaptor_removal_paired.nf \
+  -c src/nf_modules/cutadapt/cutadapt.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/cutadapt/test/adaptor_removal_single.nf \
+  -c src/nf_modules/cutadapt/cutadapt.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/cutadapt/test/trimming_paired.nf \
+  -c src/nf_modules/cutadapt/cutadapt.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/cutadapt/test/trimming_single.nf \
+  -c src/nf_modules/cutadapt/cutadapt.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"

src/nf_modules/cutadapt/tests/trimming_paired.nf

+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process trimming {
+  tag "$pair_id"
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+  file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -q 20,20 \
+  -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}
+

src/nf_modules/cutadapt/tests/trimming_single.nf

+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process trimming {
+  tag "$reads.baseName"
+
+  input:
+  file reads from fastq_files
+
+  output:
+  file "*_trim.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -q 20,20 \
+  -o ${reads.baseName}_trim.fastq.gz \
+  ${reads} > ${reads.baseName}_report.txt
+  """
+}
+