src/singularity_modules/umitools/0.3.4/build.sh

-#/bin/sh
-sudo singularity build --force bin/umitools:0.3.4.sif docker://quay.io/biocontainers/umitools:0.3.4--py37_1 && \
-singularity sign bin/umitools:0.3.4.sif

src/singularity_modules/umitools/0.3.4/umitools.def

-Bootstrap: docker
-From: ubuntu:18.04
-%labels
-MAINTAINER Laurent Modolo
-%post
-
-UMITOOLS_VERSION=0.3.4
-PACKAGES="git \
-build-essential \
-python-pip \
-ca-certificates \
-python-setuptools \
-python-dev \
-python-numpy \
-python-wheel \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip install umitools==${UMITOOLS_VERSION}
-
-%environment
-export UMITOOLS_VERSION=0.3.4
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/urqt/d62c1f8/build.sh

-#/bin/sh
-sudo singularity build --force bin/urqt:d62c1f8.sif src/singularity_modules/urqt/d62c1f8/urqt.def && \
-singularity sign bin/urqt:d62c1f8.sif

src/singularity_modules/urqt/d62c1f8/urqt.def

-Bootstrap: library
-From: debian:9
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-URQT_VERSION=d62c1f8
-PACKAGES="git \
-g++ \
-make \
-ca-certificates \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/l-modolo/UrQt.git && \
-cd UrQt && \
-git checkout ${URQT_VERSION} && \
-make && \
-cd .. && \
-mv UrQt/UrQt /usr/bin/ && \
-rm -Rf UrQt
-
-%environment
-export URQT_VERSION=d62c1f8
-
-%runscript
-exec /bin/bash "$@"

src/solution_RNASeq.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+nextflow.enable.dsl=2
+
+include { fastp } from "./nf_modules/fastp/main.nf"
+include { fasta_from_bed } from "./nf_modules/bedtools/main.nf"
+include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf' addParams(mapping_fastq_out: "quantification/")
+
+
+params.fastq = "data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files: ${params.fastq}"
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+channel
+  .fromFilePairs( params.fastq, size: -1)
+  .set { fastq_files }
+
+channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .map { it -> [it.simpleName, it]}
+  .set { fasta_files }
+channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+  .map { it -> [it.simpleName, it]}
+  .set { bed_files }
+
+workflow {
+  fastp(fastq_files)
+  fasta_from_bed(fasta_files, bed_files)
+  index_fasta(fasta_from_bed.out.fasta)
+  mapping_fastq(index_fasta.out.index.collect(), fastp.out.fastq)
+}

src/training_dataset.config

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 profiles {
   docker {
-    docker.temp = 'auto'
+    docker.temp = "auto"
     docker.enabled = true
     process {
       withName: build_synthetic_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: build_synthetic_bed {
-        container = "file://bin/bedtools:2.25.0.sif"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.sif"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -117,123 +122,252 @@ profiles {
   psmn {
     process{
       withName: build_synthetic_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128'
+        queue = "monointeldeb128"
       }
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
-        queue = 'monointeldeb128'
+        queue = "monointeldeb128"
       }
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "20GB"
         time = "12h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: mapping_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: bam_2_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: sort_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: index_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: mapping_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: bam_2_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: sort_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
       }
       withName: index_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
+        cpus = 32
         memory = "30GB"
         time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        penv = "openmp32"
+      }
+    }
+  }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+    }
+    process{
+      withName: build_synthetic_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: index_fasta {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: mapping_fastq_paired {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: bam_2_fastq_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: sort_bam_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: index_bam_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: mapping_fastq_single {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: bam_2_fastq_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: sort_bam_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
+      }
+      withName: index_bam_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = "huge"
       }
     }
   }

src/training_dataset.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 /*
 small pipeline to build a training dataset from whole genome data
 

src/update_tools.sh

-#/bin/sh
-
-# A POSIX variable
-OPTIND=1
-
-# Initialize our own variables:
-tool=""
-version=""
-
-while getopts "h?v:t:p:" opt; do
-  case "${opt}" in
-  h|\?)
-    echo "update_tools.sh -t toolname -v tool_version -p tool_previous_version"
-    exit 0
-    ;;
-  v)
-    version=${OPTARG}
-    ;;
-  p)
-    prev_version=${OPTARG}
-    ;;
-  t)
-    tool=${OPTARG}
-    ;;
-  esac
-done
-
-echo "tool=${tool}, version='${version}', previous version='${version}'"
-
-docker_tool_dir="src/docker_modules/"${tool}"/"
-echo ${docker_tool_dir}
-if [ -d ${docker_tool_dir} ]; then
-  echo "docker module found for ${tool}."
-  if [ -d ${docker_tool_dir}${version} ]; then
-    echo "version already existing, skipping."
-  else
-    cp -R ${docker_tool_dir}${prev_version} ${docker_tool_dir}${version}
-    sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/Dockerfile"
-    sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/docker_init.sh"
-    echo "docker_module for ${tool}:${version}, done."
-  fi
-else
-  echo "docker module not found for '${tool}', skipping."
-fi
-
-singularity_tool_dir="src/singularity_modules/"${tool}"/"
-echo ${singularity_tool_dir}
-if [ -d ${singularity_tool_dir} ]; then
-  echo "singularity module found for $tool."
-  if [ -d ${singularity_tool_dir}${version} ]; then
-    echo "version already existing, skipping."
-  else
-    cp -R ${singularity_tool_dir}${prev_version} ${singularity_tool_dir}${version}
-    sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/${tool}.def"
-    sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/build.sh"
-    echo "singularity_module for ${tool}:${version}, done."
-  fi
-else
-  echo "singularity module not found for '${tool}', skipping."
-fi
-
-nf_tool_dir="src/nf_modules/"$tool"/"
-echo $nf_tool_dir
-if [ -d ${nf_tool_dir} ]; then
-  echo "nf module found for ${tool}."
-  find ${nf_tool_dir} -maxdepth 1 -mindepth 1 -type f -name "*.config" |
-    awk "{system(\"sed -i \\\"s|${prev_version}|${version}|g\\\" \"\$0)}"
-  echo "nf_module for ${tool}:${version}, done."
-else
-  echo "nf module not found for '${tool}', skipping."
-fi
-
-psmn_modules_dir="src/psmn_modules/.git/"
-if [ ! -d ${nf_tool_dir} ]; then
-  git submodule init && \
-  git submodule update
-fi
-psmn_tool_app_dir="src/psmn_modules/apps/"${tool}"/"
-psmn_tool_module_dir="src/psmn_modules/modulefiles/"${tool}"/"
-echo ${psmn_tool_app_dir}
-if [ -d ${psmn_tool_app_dir} ]; then
-  echo "psmn module found for ${tool}."
-  cp ${psmn_tool_app_dir}/install_${prev_version}.sh \
-    ${psmn_tool_app_dir}/install_${version}.sh
-  sed -i "s|$prev_version|$version|g" ${psmn_tool_app_dir}/install_${version}.sh
-  cp ${psmn_tool_module_dir}/${prev_version}.lua \
-    ${psmn_tool_module_dir}/${version}.lua
-  sed -i "s|${prev_version}|${version}|g" ${psmn_tool_module_dir}/${version}.lua
-  echo "psmn_module for ${tool}:${version}, done."
-else
-  echo "psmn module not found for '${tool}', skipping."
-fi