src/nf_modules/HTSeq/htseq.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $counting {
-        container = "htseq:0.8.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load HTSeq/0.8.0"
-      }
-    }
-  }
-}

src/nf_modules/HTSeq/htseq.nf

-/*
-* htseq :
-* Imputs : sorted bams files
-* Imputs : gtf
-* Output : counts files
-*/
-/*                      quality trimming                                     */
-
-params.bam = "$baseDir/data/bam/*.bam"
-params.gtf = "$baseDir/data/annotation/*.gtf"
-
-log.info "bam files : ${params.bam}"
-log.info "gtf files : ${params.gtf}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
-  .set { bam_files }
-Channel
-  .fromPath( params.gtf )
-  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
-  .set { gtf_file }
-
-process counting {
-  tag "$bam.baseName"
-  publishDir "results/quantification/", mode: 'copy'
-
-  input:
-  file bam from bam_files
-  file gtf from gtf_file
-
-  output:
-  file "*.count" into count_files
-
-  script:
-"""
-htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
---format=bam ${bam} ${gtf} > ${bam.baseName}.count
-"""
-}

src/nf_modules/HTSeq/tests/counting.nf

-params.bam = "$baseDir/data/bam/*.bam"
-params.gtf = "$baseDir/data/annotation/*.gtf"
-
-log.info "bam files : ${params.bam}"
-log.info "gtf files : ${params.gtf}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
-  .set { bam_files }
-Channel
-  .fromPath( params.gtf )
-  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
-  .set { gtf_file }
-
-process counting {
-  tag "$bam.baseName"
-  publishDir "results/quantification/", mode: 'copy'
-
-  input:
-  file bam from bam_files
-  file gtf from gtf_file
-
-  output:
-  file "*.count" into count_files
-
-  script:
-"""
-htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
---format=bam ${bam} ${gtf} > ${bam.baseName}.count
-"""
-}
-

src/nf_modules/HTSeq/tests/tests.sh

-nextflow src/nf_modules/HTSeq/tests/counting.nf \
-  -c src/nf_modules/HTSeq/htseq.config \
-  -profile docker \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-

src/nf_modules/Kallisto/kallisto.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "kallisto:0.44.0"
-      }
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}

src/nf_modules/Kallisto/kallisto.nf

-/*
-* Kallisto :
-* 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 fasta files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$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: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into counts_files
-
-  script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
-"""
-}
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 200
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-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/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  script:
-"""
-mkdir ${reads.baseName}
-kallisto quant -i ${index} -t ${task.cpus} --single
---bias --bootstrap-samples 100 -o ${reads.baseName} \
--l ${params.mean} -s ${params.sd} -o ./ \
-${reads} > ${reads.baseName}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/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
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/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: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into counts_files
-
-  script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/tests/mapping_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 200
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-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/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  script:
-"""
-mkdir ${reads.baseName}
-kallisto quant -i ${index} -t ${task.cpus} --single \
---bias --bootstrap-samples 100 -o ${reads.baseName} \
--l ${params.mean} -s ${params.sd} \
-${reads} > ${reads.baseName}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/tests/tests.sh

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

src/nf_modules/MultiQC/multiqc.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-      $multiqc {
-        container = "multiqc:1.0"
-      }
-    }
-  }
-  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'
-      }
-      $multiqc {
-        beforeScript = "module purge; module load FastQC/1.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}

src/nf_modules/MultiQC/multiqc.nf

-/*
-* multiqc :
-* Imputs : report files
-* Output :  multiqc report
-*/
-
-/*                      MultiQC                                     */
-
-process multiqc {
-  tag "$report.baseName"
-  publishDir "results/fastq/multiqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file report from fastqc_report.collect()
-
-  output:
-    file "*multiqc_*" into multiqc_report
-
-  script:
-"""
-multiqc -f .
-"""
-}
-

src/nf_modules/MultiQC/tests/multiqc_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]} ${reads[1]}
-"""
-}
-
-process multiqc {
-  tag "$report[0].baseName"
-  publishDir "results/fastq/multiqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file report from fastqc_report.collect()
-
-  output:
-    file "*multiqc_*" into multiqc_report
-
-  script:
-"""
-multiqc -f .
-"""
-}
-

src/nf_modules/MultiQC/tests/multiqc_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 ./ ${reads}
-"""
-}
-
-process multiqc {
-  tag "$report[0].baseName"
-  publishDir "results/fastq/multiqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file report from fastqc_report.collect()
-
-  output:
-    file "*multiqc_*" into multiqc_report
-
-  script:
-"""
-multiqc -f .
-"""
-}
-

src/nf_modules/MultiQC/tests/tests.sh

-nextflow src/nf_modules/MultiQC/tests/multiqc_paired.nf \
-  -c src/nf_modules/MultiQC/multiqc.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/MultiQC/tests/multiqc_single.nf \
-  -c src/nf_modules/MultiQC/multiqc.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"

src/nf_modules/RSEM/rsem.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "rsem:1.3.0"
-      }
-      $mapping_fastq {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
-      }
-      $mapping_fastq {
-        beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
-      }
-    }
-  }
-}

src/nf_modules/RSEM/rsem.nf

-/*
-* RSEM :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/*                      fasta indexing                                     */
-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gff3"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_file }
-Channel
-  .fromPath( params.annotation )
-  .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
-  .set { annotation_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-    file annotation from annotation_file
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-  def cmd_annotation = "--gff3 ${annotation}"
-  if(annotation ==~ /.*\.gtf$/){
-    cmd_annotation = "--gtf ${annotation}"
-  }
-"""
-rsem-prepare-reference -p ${task.cpus} --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
-${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
-${fasta.baseName}_rsem_bowtie2_report.txt
-"""
-}
-
-
-/*
-* 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/quantification/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into counts_files
-
-  script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
--output-genome-bam -p ${task.cpus} \
---paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
-> ${pair_id}_rsem_bowtie2_report.txt
-"""
-}
-
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 300
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-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/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
---fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
---output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${tagname} > ${tagname}_rsem_bowtie2_report.txt
-"""
-}
-

src/nf_modules/RSEM/tests/index.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gff3"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_file }
-Channel
-  .fromPath( params.annotation )
-  .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
-  .set { annotation_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-    file annotation from annotation_file
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-  def cmd_annotation = "--gff3 ${annotation}"
-  if(annotation ==~ /.*\.gtf$/){
-    cmd_annotation = "--gtf ${annotation}"
-  }
-"""
-rsem-prepare-reference -p ${task.cpus} --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
-${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
-${fasta.baseName}_rsem_bowtie2_report.txt
-"""
-}
-
-

src/nf_modules/RSEM/tests/quantification_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/quantification/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into counts_files
-
-  script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
--output-genome-bam -p ${task.cpus} \
---paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
-> ${pair_id}_rsem_bowtie2_report.txt
-"""
-}
-
-

src/nf_modules/RSEM/tests/quantification_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 300
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-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/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
---fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
---output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${reads.baseName} \
-> ${reads.baseName}_rsem_bowtie2_report.txt
-"""
-}
-