src/nf_modules/BEDtools/bedtools.nf

-/*
-* bedtools :
-* Imputs : fasta files
-* Imputs : bed files
-* Output : fasta files
-*/
-/*                      fasta extraction                                     */
-
-params.fasta = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_files }
-Channel
-  .fromPath( params.bed )
-  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
-  .set { bed_files }
-
-process fasta_from_bed {
-  tag "${bed.baseName}"
-  cpus 4
-  publishDir "results/fasta/", mode: 'copy'
-
-  input:
-  file fasta from fasta_files
-  file bed from bed_files
-
-  output:
-  file "*_extracted.fasta" into fasta_files_extracted
-
-  script:
-"""
-bedtools getfasta -name \
--fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
-"""
-}

src/nf_modules/BEDtools/tests/fasta_from_bed.nf

-params.fastq = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_files }
-Channel
-  .fromPath( params.bed )
-  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
-  .set { bed_files }
-
-process fasta_from_bed {
-  tag "${bed.baseName}"
-  cpus 4
-  publishDir "results/fasta/", mode: 'copy'
-
-  input:
-  file fasta from fasta_files
-  file bed from bed_files
-
-  output:
-  file "*_extracted.fasta" into fasta_files_extracted
-
-  script:
-"""
-bedtools getfasta -name \
--fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
-"""
-}

src/nf_modules/BEDtools/tests/tests.sh

-nextflow src/nf_modules/BEDtools/tests/fasta_from_bed.nf \
-  -c src/nf_modules/BEDtools/bedtools.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \

src/nf_modules/Bowtie/bowtie.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie:1.2.2"
-      }
-      $mapping_fastq {
-        container = "bowtie:1.2.2"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie/1.2.2"
-      }
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
-      }
-    }
-  }
-}

src/nf_modules/Bowtie/bowtie.nf

-/*
-* Bowtie :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/*                      fasta indexing                                     */
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
-        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
-    }
-  }
-"""
-# -v specify the max number of missmatch, -k the number of match reported per
-# reads
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-/*
-* for single-end data
-*/
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-index_id = index[0]
-for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
-      index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
-  }
-}
-"""
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--q ${reads} 2> \
-${reads.baseName}_bowtie_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie/tests/index.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-

src/nf_modules/Bowtie/tests/mapping_paired.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
-        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
-    }
-  }
-"""
-# -v specify the max number of missmatch, -k the number of match reported per
-# reads
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-
-

src/nf_modules/Bowtie/tests/mapping_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-index_id = index[0]
-for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
-      index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
-  }
-}
-"""
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--q ${reads} 2> \
-${reads.baseName}_bowtie_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie/tests/tests.sh

-./nextflow src/nf_modules/Bowtie/tests/index.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie/tests/mapping_single.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie/tests/mapping_paired.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-

src/nf_modules/Bowtie2/bowtie2.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie2:2.3.4.1"
-      }
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
-      }
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}

src/nf_modules/Bowtie2/bowtie2.nf

-/*
-* Bowtie2 :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/*                      fasta indexing                                     */
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  set pair_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie2/tests/index.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-

src/nf_modules/Bowtie2/tests/mapping_paired.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  set pair_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-

src/nf_modules/Bowtie2/tests/mapping_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie2/tests/tests.sh

-./nextflow src/nf_modules/Bowtie2/tests/index.nf \
-  -c src/nf_modules/Bowtie2/bowtie2.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie2/tests/mapping_single.nf \
-  -c src/nf_modules/Bowtie2/bowtie2.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie2/tests/mapping_paired.nf \
-  -c src/nf_modules/Bowtie2/bowtie2.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-

src/nf_modules/FastQC/fastqc.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}

src/nf_modules/FastQC/fastqc.nf

-/*
-* fastqc :
-* Imputs : fastq files
-* Output : pdf files
-*/
-
-/*                      fastQC                                     */
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$reads.baseName"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file reads from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$pair_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-

src/nf_modules/FastQC/tests/fastqc_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: ${params.fastq}" }
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$pair_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-

src/nf_modules/FastQC/tests/fastqc_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: ${params.fastq}" }
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$reads.baseName"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file reads from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-

src/nf_modules/FastQC/tests/tests.sh

-nextflow src/nf_modules/FastQC/tests/fastqc_paired.nf \
-  -c src/nf_modules/FastQC/fastqc.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/FastQC/tests/fastqc_single.nf \
-  -c src/nf_modules/FastQC/fastqc.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"