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
-"""
-}
-

src/nf_modules/RSEM/tests/tests.sh

-nextflow src/nf_modules/RSEM/tests/index.nf \
-  -c src/nf_modules/RSEM/rsem.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gff"
-
-nextflow src/nf_modules/RSEM/tests/quantification_single.nf \
-  -c src/nf_modules/RSEM/rsem.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-nextflow src/nf_modules/RSEM/tests/quantification_paired.nf \
-  -c src/nf_modules/RSEM/rsem.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-

src/nf_modules/SAMtools/1.7/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/SAMtools/1.7 -t 'samtools:1.7'

src/nf_modules/SAMtools/samtools.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam {
-        container = "samtools:1.7"
-      }
-      $index_bam {
-        container = "samtools:1.7"
-      }
-      $split_bam {
-        container = "samtools:1.7"
-      }
-      $filter_bam {
-        container = "samtools:1.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-      $index_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-      $split_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-      $filter_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-    }
-  }
-}

src/nf_modules/SAMtools/samtools.nf

-/*
-* SAMtools :
-* Imputs : bam files
-* Output : bam files
-*/
-
-/*                      bams sorting                                     */
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process sort_bam {
-  tag "$bam.baseName"
-  cpus 4
-
-  input:
-    file bam from bam_files
-
-  output:
-    file "*_sorted.bam" into sorted_bam_files
-
-  script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
-"""
-}
-
-/*                      bams indexing                                     */
-
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process index_bam {
-  tag "$bam.baseName"
-  input:
-    file bam from bam_files
-  output:
-    file "*bam*" into indexed_bam_file
-  script:
-"""
-samtools index ${bam}
-"""
-}
-
-
-/*                      bams spliting                                     */
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process split_bam {
-  tag "$bam.baseName"
-  cpus 2
-
-  input:
-    file bam from bam_files
-
-  output:
-    file "*_forward.bam*" into forward_bam_files
-    file "*_reverse.bam*" into reverse_bam_files
-  script:
-"""
-samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
-"""
-}
-
-
-/*                      bams filtering                                     */
-params.bam = "$baseDir/data/bam/*.bam"
-params.bed = "$baseDir/data/bam/*.bed"
-
-log.info "bams files : ${params.bam}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-Channel
-  .fromPath( params.bed )
-  .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
-  .set { bed_files }
-
-process filter_bam {
-  tag "$bam.baseName"
-  cpus 4
-
-  input:
-    file bam from bam_files
-    file bed from bed_files
-
-  output:
-    file "*_filtered.bam*" into filtered_bam_files
-  script:
-"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
-"""
-}
-
-

src/nf_modules/SAMtools/tests/filter_bams.nf

-params.bam = "$baseDir/data/bam/*.bam"
-params.bed = "$baseDir/data/bam/*.bed"
-
-log.info "bams files : ${params.bam}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-Channel
-  .fromPath( params.bed )
-  .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
-  .set { bed_files }
-
-process filter_bam {
-  tag "$bam.baseName"
-  cpus 4
-
-  input:
-    file bam from bam_files
-    file bed from bed_files
-
-  output:
-    file "*_filtered.bam*" into filtered_bam_files
-  script:
-"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
-"""
-}
-
-

src/nf_modules/SAMtools/tests/index_bams.nf

-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process index_bam {
-  tag "$bam.baseName"
-  input:
-    file bam from bam_files
-  output:
-    file "*bam*" into indexed_bam_file
-  script:
-"""
-samtools index ${bam}
-"""
-}
-

src/nf_modules/SAMtools/tests/sort_bams.nf

-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process sort_bam {
-  tag "$bams.baseName"
-  cpus 4
-
-  input:
-    file bam from bam_files
-
-  output:
-    file "*_sorted.bam" into sorted_bam_files
-
-  script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
-"""
-}
-

src/nf_modules/SAMtools/tests/split_bams.nf

-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .set { bam_files }
-
-process split_bam {
-  tag "$bam.baseName"
-  cpus 2
-
-  input:
-    file bam from bam_files
-
-  output:
-    file "*_forward.bam*" into forward_bam_files
-    file "*_reverse.bam*" into reverse_bam_files
-  script:
-"""
-samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
-"""
-}
-

src/nf_modules/SAMtools/tests/tests.sh

-nextflow src/nf_modules/SAMtools/tests/sort_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-nextflow src/nf_modules/SAMtools/tests/index_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-
-nextflow src/nf_modules/SAMtools/tests/split_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-nextflow src/nf_modules/SAMtools/tests/filter_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  --bed "data/tiny_dataset/OLD/2genes.bed"

src/nf_modules/SRAtoolkit/2.8.2/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'

src/nf_modules/Salmon/0.8.2/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/Salmon/0.8.2 -t 'salmon:0.8.2'

src/nf_modules/TopHat/2.1.1/Dockerfile

-FROM ubuntu:18.04
-MAINTAINER Laurent Modolo
-
-ENV TOPHAT_VERSION=2.1.1
-ENV PACKAGES tophat=${BOWTIE2_VERSION}*
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean

src/nf_modules/TopHat/2.1.1/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/TopHat/2.1.1 -t 'tophat:2.1.1'

src/nf_modules/Trimmomatic/0.36/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/Trimmomatic/0.36 -t 'trimmomatic:0.36'

src/nf_modules/UrQt/d62c1f8/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/UrQt/d62c1f8 -t 'urqt:62c1f8'

src/nf_modules/UrQt/tests/tests.sh

-nextflow src/nf_modules/UrQt/tests/trimming_paired.nf \
-  -c src/nf_modules/UrQt/urqt.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/UrQt/tests/trimming_single.nf \
-  -c src/nf_modules/UrQt/urqt.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"

src/nf_modules/UrQt/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"
-  cpus 4
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
-
-  script:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads[0]} --inpair ${reads[1]} \
---out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
-> ${pair_id}_trimming_report.txt
-"""
-}

src/nf_modules/UrQt/tests/trimming_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: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$reads.baseName"
-  cpus 4
-
-  input:
-  file reads from fastq_files
-
-  output:
-  file "*_trim.fastq.gz" into fastq_files_trim
-
-  script:
-  """
-  UrQt --t 20 --m ${task.cpus} --gz \
-  --in ${reads} \
-  --out ${reads.baseName}_trim.fastq.gz \
-  > ${reads.baseName}_trimming_report.txt
-  """
-}
-