src/nf_modules/music/peak_calling_single.nf

-params.read_size = 100
-params.frag_size = 200
-params.step_l = 50
-params.min_l = 200
-params.max_l = 5000
-log.info "bam files : ${params.bam}"
-log.info "index files : ${params.index}"
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_files }
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process compute_mappability {
-  tag "${fasta.baseName}"
-
-  input:
-    file index from index_files.collect()
-    file fasta from fasta_files
-
-  output:
-    file "*.bin" into mappability
-    file "temp/chr_ids.txt" into chr_ids
-
-  script:
-
-"""
-generate_multimappability_signal.csh ${fasta} ${params.read_size} ./
-bash temp_map_reads.csh
-bash temp_process_mapping.csh
-"""
-}
-
-process music_preprocessing {
-  tag "${file_id}"
-
-  input:
-    set file_id, file(bam) from bam_files
-    file chr_ids from chr_ids.collect()
-
-  output:
-    set file_id, "preprocessed/*.tar" into preprocessed_bam_files
-
-  script:
-
-"""
-mkdir preprocessed
-samtools view *.bam | \
-MUSIC -preprocess SAM stdin preprocessed/
-mkdir preprocessed/sorted
-MUSIC -sort_reads preprocessed/ preprocessed/sorted/
-mkdir preprocessed/dedup
-MUSIC -remove_duplicates ./preprocessed/sorted 2 preprocessed/dedup/
-cd preprocessed
-tar -c -f ${file_id}.tar *
-"""
-}
-
-preprocessed_bam_files_control = Channel.create()
-preprocessed_bam_files_chip = Channel.create()
-preprocessed_bam_files.choice(
-  preprocessed_bam_files_control,
-  preprocessed_bam_files_chip ) { a -> a[0] =~ /.*control.*/ ? 0 : 1 }
-
-process music_computation {
-  tag "${file_id}"
-  publishDir "results/peak_calling/${file_id}", mode: 'copy'
-
-  input:
-    set file_id, file(control) from preprocessed_bam_files_chip
-    set file_id_control, file(chip) from preprocessed_bam_files_control.collect()
-    file mapp from mappability.collect()
-
-  output:
-    file "*" into music_output_forward
-    file "*.bed" into peaks_forward
-
-  script:
-
-"""
-mkdir mappability control chip
-mv ${mapp} mappability/
-tar -xf ${control} -C control/
-tar -xf ${chip} -C chip/
-
-MUSIC -get_per_win_p_vals_vs_FC -chip chip/ -control control/ \
-  -l_win_step ${params.step_l} \
-  -l_win_min ${params.min_l} -l_win_max ${params.max_l}
-MUSIC -get_multiscale_punctate_ERs \
-  -chip chip/ -control control/ -mapp mappability/ \
-  -l_mapp ${params.read_size} -l_frag ${params.frag_size} -q_val 1 -l_p 0
-ls -l
-"""
-}

src/nf_modules/music/tests.sh

-cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
-./nextflow src/nf_modules/music/peak_calling_single.nf \
-  -c src/nf_modules/music/peak_calling_single.config \
-  -profile docker \
-  --fasta "results/training/fasta/*.fasta" \
-  --bam "results/training/bams/s*.bam" \
-  --index "results/training/mapping/index/*" \
-  --read_size 50 --frag_size 300

src/nf_modules/picard/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "2.18.11"
+container_url = "lbmc/picard:${version}"
+
+params.mark_duplicate = "VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true"
+params.mark_duplicate_out = ""
+process mark_duplicate {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.mark_duplicate_out != "") {
+    publishDir "results/${params.mark_duplicate_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam)
+  output:
+    tuple val(file_id) , path("*.bam"), emit: bam
+    path "*_report.dupinfo.txt", emit: report
+
+
+  script:
+"""
+PicardCommandLine MarkDuplicates \
+  ${params.mark_duplicate} \
+  INPUT=${bam} \
+  OUTPUT=${bam.baseName}_dedup.bam \
+  METRICS_FILE=${bam.baseName}_picard_dedup_report.dupinfo.txt &> \
+  picard_${bam.baseName}.log
+"""
+}
+
+params.normalize_fasta = ""
+params.normalize_fasta_out = ""
+process normalize_fasta {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.normalize_fasta_out != "") {
+    publishDir "results/${params.normalize_fasta_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fasta)
+  output:
+    tuple val(file_id), path("results/*.fasta.gz"), emit: fasta 
+
+  script:
+"""
+mkdir -p results
+PicardCommandLine NormalizeFasta \
+      I=${fasta} \
+      O=results/${fasta.simpleName}.fasta
+gzip results/${fasta.simpleName}.fasta
+"""
+}
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${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("*.dict"), emit: index
+
+  script:
+"""
+PicardCommandLine CreateSequenceDictionary \
+  ${params.index_fasta} \
+  REFERENCE=${fasta} \
+  OUTPUT=${fasta.baseName}.dict
+"""
+}
+
+params.index_bam = ""
+params.index_bam_out = ""
+process index_bam {
+  container = "${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("*"), emit: index
+
+  script:
+"""
+PicardCommandLine BuildBamIndex \
+  ${params.index_bam} \
+  INPUT=${bam}
+"""
+}

src/nf_modules/porechop/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.2.4"
+container_url = "lbmc/porechop:${version}"
+
+process porechop {
+    container = "${container_url}"
+    label "big_mem_multi_cpus"
+    tag "$file_id"
+    if (params.porechop_out != "") {
+    publishDir "results/${params.porechop_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fatsq)
+
+  output:
+    tuple val(file_id), path("*_porechoped.fastq"), emit: porechoped_fastq
+  script:
+"""
+porechop -i ${fastq} -o ${file_id}_porechoped.fastq --threads 4
+"""
+}
\ No newline at end of file

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/rsem/indexing.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      withName: index_fasta {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  psmn {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
-        executor = "sge"
-        clusterOptions = "-m e -cwd -V"
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
-      }
-    }
-  }
-}

src/nf_modules/rsem/indexing.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gff3"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_file }
-Channel
-  .fromPath( params.annotation )
-  .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
-  .set { annotation_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-    file annotation from annotation_file
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-  def cmd_annotation = "--gff3 ${annotation}"
-  if(annotation ==~ /.*\.gtf$/){
-    cmd_annotation = "--gtf ${annotation}"
-  }
-"""
-rsem-prepare-reference -p ${task.cpus} --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
-${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
-${fasta.baseName}_rsem_bowtie2_report.txt
-"""
-}
-
-

src/nf_modules/rsem/quantification_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      withName: mapping_fastq {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  psmn {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
-        executor = "sge"
-        clusterOptions = "-m e -cwd -V"
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
-      }
-    }
-  }
-}

src/nf_modules/rsem/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_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[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_id} ${pair_id} \
-2> ${pair_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${pair_id}_rsem_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-

src/nf_modules/rsem/quantification_single.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      withName: mapping_fastq {
-        container = "rsem:1.3.0"
-      }
-    }
-  }
-  psmn {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
-        executor = "sge"
-        clusterOptions = "-m e -cwd -V"
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
-      }
-    }
-  }
-}

src/nf_modules/rsem/quantification_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 200
-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}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.toList()
-
-  output:
-  file "*" into count_files
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-ls -l
-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_id} ${file_id} \
-2> ${file_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${file_id}_rsem_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-

src/nf_modules/rsem/tests.sh

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

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 {
-      withName: index_bam {
-        container = "sambamba:0.6.7"
-        cpus = 4
-      }
-    }
-  }
-  singularity {
-    singularity.enabled = true
-    process {
-      withName: index_bam {
-        container = "file://bin/sambamba:0.6.7.sif"
-        cpus = 4
-      }
-    }
-  }
-  psmn {
-    process{
-      withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.7"
-        executor = "sge"
-        clusterOptions = "-m e -cwd -V"
-        cpus = 16
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
-      }
-    }
-  }
-}

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"
-
-  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 {
-      withName: sort_bam {
-        container = "sambamba:0.6.7"
-        cpus = 4
-      }
-    }
-  }
-  singularity {
-    singularity.enabled = true
-    process {
-      withName: sort_bam {
-        container = "file://bin/sambamba:0.6.7.sif"
-        cpus = 4
-      }
-    }
-  }
-  psmn {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.7"
-        executor = "sge"
-        clusterOptions = "-m e -cwd -V"
-        cpus = 4
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
-      }
-    }
-  }
-}

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}
-"""
-}
-