src/docker_modules/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/docker_modules/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/docker_modules/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/docker_modules/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/docker_modules/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/docker_modules/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/docker_modules/nf_modules/Trimmomatic/0.36/docker_init.sh

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

src/docker_modules/nf_modules/UrQt/d62c1f8/docker_init.sh

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

src/docker_modules/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/docker_modules/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/docker_modules/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
-  """
-}
-

src/docker_modules/nf_modules/UrQt/urqt.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
-      }
-    }
-  }
-}

src/docker_modules/nf_modules/UrQt/urqt.nf

-/*
-* urqt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-/*                      quality trimming                                     */
-
-/*
-* 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: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  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 \
-> ${pair_id}_trimming_report.txt
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  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
-"""
-}
-

src/docker_modules/nf_modules/canu/1.6/docker_init.sh

-#!/bin/sh
-docker build src/nf_modules/canu/1.6 -t 'canu:1.6'

src/docker_modules/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/docker_modules/nf_modules/cutadapt/1.14/docker_init.sh

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

src/docker_modules/nf_modules/cutadapt/cutadapt.config

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

src/docker_modules/nf_modules/cutadapt/cutadapt.nf

-/*
-* cutadapt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-
-/*                      Illumina adaptor removal                             */
-
-/*
-* 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: ${params.fastq}" }
-  .set { fastq_files }
-
-process adaptor_removal {
-  tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
-  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]} > ${pair_id}_report.txt
-  """
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process adaptor_removal {
-  tag "$reads.baseName"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
-  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} > ${reads.baseName}_report.txt
-  """
-}
-
-/*                      quality trimming                                     */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$pair_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  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]} > ${pair_id}_report.txt
-  """
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$reads.baseName"
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  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
-  """
-}
-

src/docker_modules/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/docker_modules/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
-  """
-}
-