src/nf_modules/Kallisto/indexing.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 "*_kallisto_report.txt" into index_files_report
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-2> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/mapping_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $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/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.collect()
-
-  output:
-  file "*" into counts_files
-
-  script:
-"""
-mkdir ${pair_id}
-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/mapping_single.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $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/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}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  file "*" into count_files
-
-  script:
-"""
-mkdir ${file_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
---bias --bootstrap-samples 100 -o ${file_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} &> ${file_id}/kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/tests.sh

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

src/nf_modules/MUSIC/peak_calling_single.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $compute_mappability {
-        container = "music:6613c53"
-      }
-      $music_preprocessing {
-        container = "music:6613c53"
-      }
-      $music_computation {
-        container = "music:6613c53"
-      }
-    }
-  }
-  sge {
-    process{
-      $compute_mappability {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_preprocessing {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_computation {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-    }
-  }
-}

src/nf_modules/MUSIC/peak_calling_single.nf

-params.read_size = 100
-params.frag_size = 200
-params.step_l = 50
-params.min_l = 200
-params.max_l = 5000
-log.info "bam files : ${params.bam}"
-log.info "index files : ${params.index}"
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_files }
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process compute_mappability {
-  tag "${fasta.baseName}"
-
-  input:
-    file index from index_files.collect()
-    file fasta from fasta_files
-
-  output:
-    file "*.bin" into mappability
-    file "temp/chr_ids.txt" into chr_ids
-
-  script:
-
-"""
-generate_multimappability_signal.csh ${fasta} ${params.read_size} ./
-bash temp_map_reads.csh
-bash temp_process_mapping.csh
-"""
-}
-
-process music_preprocessing {
-  tag "${file_id}"
-
-  input:
-    set file_id, file(bam) from bam_files
-    file chr_ids from chr_ids.collect()
-
-  output:
-    set file_id, "preprocessed/*.tar" into preprocessed_bam_files
-
-  script:
-
-"""
-mkdir preprocessed
-samtools view *.bam | \
-MUSIC -preprocess SAM stdin preprocessed/
-mkdir preprocessed/sorted
-MUSIC -sort_reads preprocessed/ preprocessed/sorted/
-mkdir preprocessed/dedup
-MUSIC -remove_duplicates ./preprocessed/sorted 2 preprocessed/dedup/
-cd preprocessed
-tar -c -f ${file_id}.tar *
-"""
-}
-
-preprocessed_bam_files_control = Channel.create()
-preprocessed_bam_files_chip = Channel.create()
-preprocessed_bam_files.choice(
-  preprocessed_bam_files_control,
-  preprocessed_bam_files_chip ) { a -> a[0] =~ /.*control.*/ ? 0 : 1 }
-
-process music_computation {
-  tag "${file_id}"
-  publishDir "results/peak_calling/${file_id}", mode: 'copy'
-
-  input:
-    set file_id, file(control) from preprocessed_bam_files_chip
-    set file_id_control, file(chip) from preprocessed_bam_files_control.collect()
-    file mapp from mappability.collect()
-
-  output:
-    file "*" into music_output_forward
-    file "*.bed" into peaks_forward
-
-  script:
-
-"""
-mkdir mappability control chip
-mv ${mapp} mappability/
-tar -xf ${control} -C control/
-tar -xf ${chip} -C chip/
-
-MUSIC -get_per_win_p_vals_vs_FC -chip chip/ -control control/ \
-  -l_win_step ${params.step_l} \
-  -l_win_min ${params.min_l} -l_win_max ${params.max_l}
-MUSIC -get_multiscale_punctate_ERs \
-  -chip chip/ -control control/ -mapp mappability/ \
-  -l_mapp ${params.read_size} -l_frag ${params.frag_size} -q_val 1 -l_p 0
-ls -l
-"""
-}

src/nf_modules/MUSIC/tests.sh

-cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
-./nextflow src/nf_modules/MUSIC/peak_calling_single.nf \
-  -c src/nf_modules/MUSIC/peak_calling_single.config \
-  -profile docker \
-  --fasta "results/training/fasta/*.fasta" \
-  --bam "results/training/bams/s*.bam" \
-  --index "results/training/mapping/index/*" \
-  --read_size 50 --frag_size 300

src/nf_modules/MultiQC/multiqc_paired.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_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/multiqc_single.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_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: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$file_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    set file_id, 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.sh

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

src/nf_modules/RSEM/indexing.config

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

src/nf_modules/RSEM/indexing.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/quantification_paired.config

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

src/nf_modules/RSEM/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_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]
-    }
-  }
-"""
-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_id} ${pair_id} \
-2> ${pair_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${pair_id}_rsem_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-

src/nf_modules/RSEM/quantification_single.config

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

src/nf_modules/RSEM/quantification_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}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  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]
-    }
-  }
-"""
-ls -l
-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_id} ${file_id} \
-2> ${file_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${file_id}_rsem_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-