src/.docker_modules/umi_tools/1.0.0/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/umi_tools:1.0.0
+# docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
+# docker push lbmc/umi_tools:1.0.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/umi_tools:1.0.0" --push src/.docker_modules/umi_tools/1.0.0

src/docker_modules/UrQt/d62c1f8/Dockerfile → src/.docker_modules/urqt/d62c1f8/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
-ENV PACKAGES git=1:2.17.0* \
+ENV URQT_VERSION=d62c1f8
+ENV PACKAGES git=1:2.17* \
    build-essential=12.4* \
    ca-certificates=20180409 \
+   procps \
    zlib1g-dev=1:1.2.11*
 
 RUN apt-get update && \

src/.docker_modules/urqt/d62c1f8/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/urqt:d62c1f8
+# docker build src/.docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
+# docker push lbmc/urqt:d62c1f8
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/urqt:d62c1f8" --push src/.docker_modules/urqt/d62c1f8

src/.singularity_in2p3

+/sps/lbmc/common/singularity/
\ No newline at end of file

src/.singularity_psmn

+/Xnfs/abc/singularity/
\ No newline at end of file

src/10_ribowave.nf

-/*
-* Ribowave :
-* Inputs : gtf genome files
-* Inputs : bam file
-* Inputs : genome size file
-*/
-
-/* 		PARAMETERS		 */
-
-params.gtf = ""
-params.genome = ""
-params.bam = ""
-params.genomesize = ""
-
-log.info "gtf file : ${params.gtf}"
-log.info "genome fasta file : ${params.genome}"
-log.info "bam file(s) : ${params.bam}"
-log.info "genomesize file : ${params.genomesize}"
-
-Channel
-  .fromPath( params.gtf )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.gtf}" }
-  .set { gtf_file }
-Channel
-  .fromPath( params.genome )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.genome}" }
-  .set { genome_file }
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
-  .set { bam_files }
-bam_files.into {bam_deter_P_site ; bam_track_P_site}
-Channel
-  .fromPath( params.genomesize )
-  .ifEmpty { error "Cannot find any index files matching: ${params.genomesize}" }
-  .set { genomesize_file }
-
-
-/*		CREATE ANNOTATION		*/
-
-process create_annot {
-  publishDir "results/ribowave/annotation", mode: 'copy'
-
-  input:
-    file gtf from gtf_file
-    file genome from genome_file
-
-  output:
-    file "*" into annot_file
-    file "start_codon.bed" into start_codon_channel
-    file "final.ORFs" into finalORF_channel
-    file "exons.gtf" into exon_gtf_channel
-
-  script:
-"""
-/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome}  -o ./  -s /Ribowave/scripts
-"""
-}
-
-
-/*		P-site determination		*/
-
-process determination_P_site {
-  tag "$bam.baseName"
-  publishDir "results/ribowave", mode: 'copy'
-
-  input:
-  file bam from bam_deter_P_site
-  file start from start_codon_channel
-
-  output:
-  file "*" into p_site_channel
-  file "*psite1nt.txt" into psite1nt_channel
-
-  script:
-"""
-/Ribowave/scripts/P-site_determination.sh -i ${bam} -S ${start} -o ./ -n ${bam.baseName} -s /Ribowave/scripts
-"""
-}
-
-/*		P-site track		*/
-
-process track_P_site {
-  tag "$bam.baseName"
-  publishDir "results/ribowave", mode: 'copy'
-
-  input:
-  file bam from bam_track_P_site
-  file exon from exon_gtf_channel
-  file genomesize from genomesize_file
-  file p_site from psite1nt_channel
-
-  output:
-  file "*" into track_p_site_channel
-  file "final.psite" into psite_channel
-  
-
-  script:
-"""
-/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genomesize} -P ${p_site} -o ./ -n ${bam.baseName} -s /Ribowave/scripts
-"""
-}
-
-/*		ribowave Identifying translated ORF		*/
-
-process ribowave_transORF {
-  publishDir "results/ribowave", mode: 'copy'
-
-  input:
-  file psite from psite_channel
-  file finalORF from finalORF_channel
-
-  output:
-  file "*" into ribowave_channel
-
-  script:
-"""
-/Ribowave/scripts/Ribowave -PD -a ${psite} -b ${finalORF} -o ./ -n ${bam.baseName} -s /Ribowave/scripts -p 2
-"""
-}
-

src/RNAseq.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq" /* we can use now a param -fastq to specify where are fastq files. this path is the default path */
-params.fasta = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fastq files : ${params.fastq}"
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-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: ${params.bed}" }
-  .set { bed_files }
-
-process adaptor_removal {
-  tag "$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]} > ${pair_id}_report.txt
-  """
-}
-
-process trimming {
-  tag "${reads}"
-  cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  input:
-  file reads from fastq_files_cut
-
-  output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
-  script:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads[0]} --inpair ${reads[1]} \
---out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
-"""
-}
-
-process fasta_from_bed {
-  tag "${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 ${bed.baseName}_extracted.fasta
-"""
-}
-
-process index_fasta {
-  tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_files_extracted
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-process mapping_fastq {
-  tag "$reads"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files_trim
-  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 ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
-"""
-}
-
-

src/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"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "urqt:d62c1f8"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fasta_from_bed {
-        container = "bedtools:2.25.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $fasta_from_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "kallisto:0.43.1"
-      }
-      $mapping_fastq {
-        container = "kallisto:0.43.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.43.1"
-        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/0.43.1"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}

src/docker_modules/BEDtools/2.25.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'

src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'

src/docker_modules/FastQC/0.11.5/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'

src/docker_modules/HTSeq/0.8.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'

src/docker_modules/Kallisto/0.43.1/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'

src/docker_modules/MultiQC/1.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/MultiQC/1.0 -t 'multiqc:1.0'

src/docker_modules/RSEM/1.3.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/RSEM/1.3.0 -t 'rsem:1.3.0'

src/docker_modules/RiboWave/1.0/Dockerfile

-FROM ubuntu:16.04
-MAINTAINER Emmanuel Labaronne
-
-ENV BEDTOOLS_VERSION=2.25.0*
-ENV PACKAGES bedtools=${BEDTOOLS_VERSION}* \
-	r-base \
-	r-base-dev \
-	git
-
-RUN apt-get update &&\ 
-	apt-get install -y --no-install-recommends ${PACKAGES} && \
-	apt-get clean
-
-RUN printf "install.packages(c('reshape','ggplot2','wmtsa','parallel'), dep=TRUE, repos='http://cran.us.r-project.org') \n source('http://bioconductor.org/biocLite.R') \n biocLite('rhdf5')" > installpackages.R && \ 
-Rscript installpackages.R
-
-RUN git clone https://github.com/lulab/Ribowave.git &&\
-	chmod -R +x Ribowave/scripts

src/docker_modules/RiboWave/1.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/RiboWave/1.0 -t 'ribowave:1.0'

src/docker_modules/SAMtools/1.7/docker_init.sh

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

src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh

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

src/docker_modules/Salmon/0.8.2/docker_init.sh

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