src/nf_modules/rasusa/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.6.0"
+container_url = "lbmc/rasusa:${version}"
+
+include { index_fasta } from "./../samtools/main.nf"
+
+params.sample_fastq = ""
+params.sample_fastq_coverage = ""
+params.sample_fastq_size = ""
+params.sample_fastq_out = ""
+workflow sample_fastq {
+  take:
+  fastq
+  fasta
+
+  main:
+  if (params.sample_fastq_coverage == "" && params.sample_fastq_size == ""){
+    fastq
+      .set{ final_fastq }
+  } else {
+    index_fasta(fasta)
+    sub_sample_fastq(fastq, index_fasta.out.index)
+    sub_sample_fastq.out.fastq
+      .set{ final_fastq }
+  }
+
+  emit:
+  fastq = final_fastq
+
+}
+
+process sub_sample_fastq {
+  container = "${container_url}"
+  label "small_mem_mono_cpus"
+  tag "$file_id"
+  if (params.index_fasta_out != "") {
+    publishDir "results/${params.sample_fastq_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fastq)
+    tuple val(index_id), path(idx)
+
+  output:
+    tuple val(file_id), path("sub_*.fastq.gz"), emit: fastq
+
+  script:
+
+  switch(file_id) {
+    case {it instanceof List}:
+      file_prefix = file_id[0]
+    break
+    case {it instanceof Map}:
+      file_prefix = file_id.values()[0]
+    break
+    default:
+      file_prefix = file_id
+    break
+  }
+
+  sample_option = "-c " + params.sample_fastq_coverage
+  if (params.sample_fastq_size != ""){
+    sample_option = "-b " + params.sample_fastq_size
+  }
+
+  if (fastq.size() == 2)
+"""
+rasusa \
+  -i ${fastq[0]} ${fastq[1]} \
+  -g ${idx} \
+  ${sample_option} \
+  -o sub_${fastq[0].simpleName}.fastq.gz sub_${fastq[1].simpleName}.fastq.gz
+"""
+  else
+"""
+rasusa \
+  -i ${fastq} \
+  -g ${idx} \
+  ${sample_option} \
+  -o sub_${fastq.simpleName}.fastq.gz
+"""
+}
\ No newline at end of file

src/nf_modules/rasusa/test.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+nextflow.enable.dsl=2
+
+/*
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
+*/
+
+params.fastq = "data/fastq/*R{1,2}*"
+params.fasta = "data/fasta/*.fasta"
+params.coverage = ""
+params.size = ""
+
+include { sample_fastq } from "./main.nf" addParams(sample_fastq_coverage: params.coverage, sample_fastq_size: params.size, sample_fastq_out: "sample/")
+
+channel
+  .fromFilePairs( params.fastq, size: -1)
+  .set { fastq_files }
+
+channel
+  .fromPath( params.fasta )
+  .map { it -> [it.simpleName, it]}
+  .set { fasta_files }
+
+workflow {
+  sample_fastq(fastq_files, fasta_files.collect())
+}
\ No newline at end of file

src/nf_modules/rasusa/test.sh

+#! /bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
\ No newline at end of file

src/nf_modules/salmon/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "1.8.0"
+container_url = "lbmc/salmon:${version}"
+
+process quantify {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.salmon_out != "") {
+    publishDir "results/${params.salmon_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.sf"), emit: quant
+  script:
+"""
+salmon quant -l A --noErrorModel -t XXXXXXXXXX -a ${bam} -p 4 -o ${params.salmon_out}
+"""
+}
\ No newline at end of file

src/nf_modules/sambamba/index_bams.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_bam {
-        container = "sambamba:0.6.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
-      }
-    }
-  }
-}

src/nf_modules/sambamba/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: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-
-process index_bam {
-  tag "$file_id"
-  cpus 4
-
-  input:
-    set file_id, file(bam) from bam_files
-
-  output:
-    set file_id, "*.bam*" into indexed_bam_file
-
-  script:
-"""
-sambamba index -t ${task.cpus} ${bam}
-"""
-}
-

src/nf_modules/sambamba/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.6.7"
+container_url = "lbmc/sambamba:${version}"
+
+params.index_bam = ""
+process index_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+sambamba index ${params.index_bam} -t ${task.cpus} ${bam}
+"""
+}
+
+params.sort_bam = ""
+process sort_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+sambamba sort -t ${task.cpus} ${params.sort_bam} -o ${bam.baseName}_sorted.bam ${bam}
+"""
+}
+
+params.split_bam = ""
+process split_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_forward.bam*"), emit: bam_forward
+    tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
+  script:
+"""
+sambamba view -t ${task.cpus} ${params.split_bam} -h -F "strand == '+'" ${bam} > \
+  ${bam.baseName}_forward.bam
+sambamba view -t ${task.cpus} ${params.split_bam} -h -F "strand == '-'" ${bam} > \
+  ${bam.baseName}_reverse.bam
+"""
+}

src/nf_modules/sambamba/sort_bams.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam {
-        container = "sambamba:0.6.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $sort_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
-      }
-    }
-  }
-}

src/nf_modules/sambamba/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: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-
-process sort_bam {
-  tag "$file_id"
-  cpus 4
-
-  input:
-    set file_id, file(bam) from bam_files
-
-  output:
-    set file_id, "*_sorted.bam" into sorted_bam_files
-
-  script:
-"""
-sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
-"""
-}
-

src/nf_modules/sambamba/split_bams.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $split_bam {
-        container = "sambamba:0.6.7"
-      }
-    }
-  }
-  sge {
-    process{
-      $split_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
-      }
-    }
-  }
-}

src/nf_modules/sambamba/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: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-
-process split_bam {
-  tag "$file_id"
-  cpus 4
-
-  input:
-    set file_id, file(bam) from bam_files
-
-  output:
-    set file_id, "*_forward.bam*" into forward_bam_files
-    set file_id, "*_reverse.bam*" into reverse_bam_files
-  script:
-"""
-sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
-sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
-"""
-}
-

src/nf_modules/sambamba/tests.sh

-./nextflow src/nf_modules/sambamba/sort_bams.nf \
-  -c src/nf_modules/sambamba/sort_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-./nextflow src/nf_modules/sambamba/index_bams.nf \
-  -c src/nf_modules/sambamba/index_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-
-./nextflow src/nf_modules/sambamba/split_bams.nf \
-  -c src/nf_modules/sambamba/split_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"

src/nf_modules/samblaster/dedup_sams.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $dedup_sam {
-        container = "samblaster:0.1.24"
-      }
-    }
-  }
-  sge {
-    process{
-      $dedup_sam {
-        beforeScript = "module purge; module load samblaster/0.1.24"
-      }
-    }
-  }
-}

src/nf_modules/samblaster/dedup_sams.nf

-params.sam = "$baseDir/data/sam/*.sam"
-
-log.info "sams files : ${params.sam}"
-
-Channel
-  .fromPath( params.sam )
-  .ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { sam_files }
-
-process dedup_sam {
-  tag "$file_id"
-  cpus 4
-
-  input:
-    set file_id, file(sam) from sam_files
-
-  output:
-    set file_id, "*_dedup.sam*" into dedup_sam_files
-  script:
-"""
-samblaster --addMateTags -i ${sam} -o ${file_id}_dedup.sam
-"""
-}
-
-

src/nf_modules/samblaster/tests.sh

-./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-  -c src/nf_modules/samblaster/dedup_sams.config \
-  -profile docker \
-  --sam "data/tiny_dataset/map/tiny_v2.sam"

src/nf_modules/samtools/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "1.11"
+container_url = "lbmc/samtools:${version}"
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.index_fasta_out != "") {
+    publishDir "results/${params.index_fasta_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fasta)
+  output:
+    tuple val(file_id), path("*.fai"), emit: index
+
+  script:
+"""
+if gzip -t ${fasta}; then
+  zcat ${fasta} > ${fasta.simpleName}.fasta
+  samtools faidx ${params.index_fasta}  ${fasta.simpleName}.fasta
+else
+  samtools faidx ${params.index_fasta} ${fasta}
+fi
+
+"""
+}
+
+params.filter_bam_quality_threshold = 30
+params.filter_bam_quality = "-q ${params.filter_bam_quality_threshold}"
+params.filter_bam_quality_out = ""
+process filter_bam_quality {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.filter_bam_quality_out != "") {
+    publishDir "results/${params.filter_bam_quality_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_filtered.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} -hb ${bam} ${params.filter_bam_quality} > \
+  ${bam.simpleName}_filtered.bam
+"""
+}
+
+params.filter_bam = ""
+params.filter_bam_out = ""
+process filter_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.filter_bam_out != "") {
+    publishDir "results/${params.filter_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+    tuple val(bed_id), path(bed)
+
+  output:
+    tuple val(file_id), path("*_filtered.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} ${params.filter_bam} > \
+  ${bam.simpleName}_filtered.bam
+"""
+}
+
+params.rm_from_bam = ""
+params.rm_from_bam_out = ""
+process rm_from_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.rm_from_bam_out != "") {
+    publishDir "results/${params.rm_from_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+    tuple val(bed_id), path(bed)
+
+  output:
+    tuple val(file_id), path("*_filtered.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} ${params.filter_bam} -hb -L ${bed} -U ${bam.simpleName}_filtered.bam ${bam} >  /dev/null
+"""
+}
+
+params.filter_bam_mapped = "-F 4"
+params.filter_bam_mapped_out = ""
+process filter_bam_mapped {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.filter_bam_mapped_out != "") {
+    publishDir "results/${params.filter_bam_mapped_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_mapped.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} ${params.filter_bam_mapped} -hb ${bam} > \
+  ${bam.simpleName}_mapped.bam
+"""
+}
+
+params.filter_bam_unmapped = "-f 4"
+params.filter_bam_unmapped_out = ""
+process filter_bam_unmapped {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.filter_bam_unmapped_out != "") {
+    publishDir "results/${params.filter_bam_unmapped_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_unmapped.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} ${params.filter_bam_unmapped} -hb ${bam} > ${bam.simpleName}_unmapped.bam
+"""
+}
+
+params.index_bam = ""
+params.index_bam_out = ""
+process index_bam {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.index_bam_out != "") {
+    publishDir "results/${params.index_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("${bam}"), path("*.bam.bai"), emit: bam_idx
+
+  script:
+"""
+samtools index ${params.index_bam} ${bam}
+"""
+}
+
+params.sort_bam = ""
+params.sort_bam_out = ""
+process sort_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.sort_bam_out != "") {
+    publishDir "results/${params.sort_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+samtools sort -@ ${task.cpus} ${params.sort_bam} -O BAM -o ${bam.simpleName}_sorted.bam ${bam}
+"""
+}
+
+params.split_bam = ""
+params.split_bam_out = ""
+process split_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.split_bam_out != "") {
+    publishDir "results/${params.split_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_forward.bam*"), emit: bam_forward
+    tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
+  script:
+"""
+samtools view -@ ${Math.round(task.cpus/2)} ${params.split_bam} \
+  -hb -F 0x10 ${bam} > ${bam.simpleName}_forward.bam &
+samtools view -@ ${Math.round(task.cpus/2)} ${params.split_bam} \
+  -hb -f 0x10 ${bam} > ${bam.simpleName}_reverse.bam
+"""
+}
+
+params.merge_bam = ""
+params.merge_bam_out = ""
+process merge_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.merge_bam_out != "") {
+    publishDir "results/${params.merge_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(first_file_id), path(first_bam)
+    tuple val(second_file_id), path(second_bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+  script:
+"""
+samtools merge -@ ${task.cpus} ${params.merge_bam} ${first_bam} ${second_bam} \
+  ${first_bam.simpleName}_${second_file.simpleName}.bam
+"""
+}
+
+params.merge_multi_bam = ""
+params.merge_multi_bam_out = ""
+process merge_multi_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.merge_multi_bam_out != "") {
+    publishDir "results/${params.merge_multi_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bams)
+
+  output:
+    tuple val(file_id), path("*_merged.bam*"), emit: bam
+  script:
+"""
+samtools merge -@ ${task.cpus} \
+  ${params.merge_multi_bam} \
+  ${bams[0].simpleName}_merged.bam \
+  ${bams}
+"""
+}
+
+params.stats_bam = ""
+params.stats_bam_out = ""
+process stats_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.stats_bam_out != "") {
+    publishDir "results/${params.stats_bam_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.tsv"), emit: tsv
+    path "*.flagstat.txt", emit: report 
+  script:
+"""
+samtools flagstat -@ ${task.cpus} ${params.stats_bam} -O tsv ${bam} > ${bam.simpleName}.flagstat.txt
+cp ${bam.simpleName}.flagstat.txt ${bam.simpleName}.tsv
+"""
+}
+
+params.flagstat_2_multiqc = ""
+params.flagstat_2_multiqc_out = ""
+process flagstat_2_multiqc {
+  tag "$file_id"
+  if (params.flagstat_2_multiqc_out != "") {
+    publishDir "results/${params.flagstat_2_multiqc_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(tsv)
+
+  output:
+    tuple val(file_id), path("*.txt"), emit: report
+"""
+mv ${tsv} ${tsv.simpleName}.flagstat.txt
+"""
+}
+
+params.idxstat_2_multiqc = ""
+params.idxstat_2_multiqc_out = ""
+process idxstat_2_multiqc {
+  tag "$file_id"
+  if (params.idxstat_2_multiqc_out != "") {
+    publishDir "results/${params.idxstat_2_multiqc_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(tsv)
+
+  output:
+    tuple val(file_id), path("*.txt"), emit: report
+"""
+mv ${tsv} ${tsv.simpleName}.idxstats.txt
+"""
+}
\ No newline at end of file

src/nf_modules/sanity/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+container_url="mlepetit/sanity:latest"
+
+params.sanity_out=""
+params.sanity=""
+
+process normalization_sanity
+        {
+
+        container="${container_url}"
+        label  "big_mem_multi_cpus"
+        if (params.sanity_out != "") {
+		publishDir "results/${params.sanity_out}", mode: 'copy'
+
+	}
+else {
+          publishDir "results/normalize_matrix/", mode: 'copy'
+
+           }
+
+	input:
+
+               tuple val(id_mtx), path(raw_filtered_mtx)   
+               
+
+        output:
+
+               tuple val(id_mtx),path("log_transcription_quotients.txt"), emit: normalize_filtered_mtx
+               tuple val(id_mtx), path("ltq_error_bars.txt")  ,emit: ltq_error
+
+        script:
+
+        """
+        Sanity -f ${raw_filtered_mtx} -n ${task.cpus} ${params.sanity} 
+        """
+        }

src/nf_modules/sratoolkit/list-srr.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/nf_modules/sratoolkit/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "3.0.0"
+container_url = "lbmc/sratoolkit:${version}"
+
+params.fastq_dump = ""
+params.fastq_dump_out = ""
+process fastq_dump {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$sra"
+  if (params.fastq_dump_out != "") {
+    publishDir "results/${params.fastq_dump_out}", mode: 'copy'
+  }
+
+  input:
+    val sra
+
+  output:
+    tuple val(sra), path("*.fastq"), emit: fastq
+
+  script:
+"""
+fastq-dump ${params.fastq_dump} --split-files --gzip ${sra}
+if [ -f ${sra}_1.fastq ]
+then
+  mv ${sra}_1.fastq ${sra}_R1.fastq
+fi
+if [ -f ${sra}_2.fastq ]
+then
+  mv ${sra}_2.fastq ${sra}_R2.fastq
+fi
+"""
+}