src/nf_modules/SAMtools/tests/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: ${params.bam}" }
-  .set { bam_files }
-
-process index_bam {
-  tag "$bam.baseName"
-  input:
-    file bam from bam_files
-  output:
-    file "*bam*" into indexed_bam_file
-  script:
-"""
-samtools index ${bam}
-"""
-}
-

src/nf_modules/SAMtools/tests/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: ${params.bam}" }
-  .set { bam_files }
-
-process sort_bam {
-  tag "$bams.baseName"
-  cpus 4
-
-  input:
-    file bam from bam_files
-
-  output:
-    file "*_sorted.bam" into sorted_bam_files
-
-  script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
-"""
-}
-

src/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/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/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/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/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/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/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: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "${reads}"
-  cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  input:
-  file reads from fastq_files
-
-  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 \
-> ${reads[0].baseName}_trimming_report.txt
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$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/nf_modules/agat/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.8.0"
+container_url = "lbmc/agat:${version}"
+
+params.gff_to_bed = ""
+params.gff_to_bed_out = ""
+process gff_to_bed {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.gff_to_bed_out != "") {
+    publishDir "results/${params.gff_to_bed_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(gff)
+  output:
+    tuple val(file_id), path("*.bed"), emit: bed
+
+  script:
+"""
+zcat ${gff} > ${gff.baseName}.gff
+agat_convert_sp_gff2bed.pl ${params.gff_to_bed} --gff ${gff.baseName}.gff -o ${gff.simpleName}.bed
+"""
+}
+
+params.gff_to_gtf = ""
+params.gff_to_gtf_out = ""
+process gff_to_gtf {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.gff_to_gtf_out != "") {
+    publishDir "results/${params.gff_to_gtf_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(gff)
+  output:
+    tuple val(file_id), path("*.gtf"), emit: gtf
+
+  script:
+"""
+zcat ${gff} > ${gff.baseName}.gff
+agat_convert_sp_gff2gtf.pl ${params.gff_to_gtf} --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf
+"""
+}
\ No newline at end of file

src/nf_modules/alntools/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "dd96682"
+container_url = "lbmc/alntools:${version}"
+
+params.bam2ec = ""
+params.bam2ec_out = ""
+process bam2ec {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.bam2ec_out != "") {
+    publishDir "results/${params.bam2ec_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(bam), path(bam_idx)
+    tuple val(transcripts_lengths_id), path(transcripts_lengths)
+
+  output:
+    tuple val(file_id), path("${bam.simpleName}.bin"), emit: bin
+    tuple val(transcripts_lengths_id), path("${transcripts_lengths}"), emit: tsv
+    tuple val(file_id), path("${bam.simpleName}_bam2ec_report.txt"), emit: report
+
+  script:
+"""
+mkdir tmp
+alntools bam2ec \
+  -c 1 ${params.bam2ec} \
+  -d ./tmp \
+  -t ${transcripts_lengths} \
+  -v \
+  ${bam} ${bam.simpleName}.bin &> \
+  ${bam.simpleName}_bam2ec_report.txt
+"""
+}
+
+params.gtf_to_transcripts_lengths = ""
+params.gtf_to_transcripts_lengths_out = ""
+process gtf_to_transcripts_lengths {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.gtf_to_transcripts_lengths != "") {
+    publishDir "results/${params.gtf_to_transcripts_lengths}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(gtf)
+
+  output:
+    tuple val(file_id), path("${gtf.simpleName}_transcripts_lengths.tsv"), emit: tsv
+
+  script:
+"""
+awk -F"[\\t;]" '
+\$3=="exon" {
+        ID=gensub(/transcript_id \\"(.*)\\"/, "\\\\1", "g", \$11); 
+        LEN[ID]+=\$5-\$4+1;
+    } 
+END{
+    for(i in LEN)
+        {print i"\\t"LEN[i]}
+    }
+' ${gtf} > ${gtf.simpleName}_transcripts_lengths.tsv
+"""
+}

src/nf_modules/beagle/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "5.1_24Aug19.3e8--hdfd78af_1"
+container_url = "quay.io/biocontainers/beagle::${version}"
+
+params.phasing = ""
+process phasing {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(vcf)
+    tuple val(ref_id), path(ref_vcf)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+beagle nthread=${task.cpus} \
+  gtgl=${vcf} \
+  ref=${ref_vcf}
+"""
+}

src/nf_modules/bedtools/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "2.25.0"
+container_url = "lbmc/bedtools:${version}"
+
+params.fasta_from_bed = "-name"
+params.fasta_from_bed_out = ""
+process fasta_from_bed {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.fasta_from_bed_out != "") {
+    publishDir "results/${params.fasta_from_bed_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(fasta_id), path(fasta)
+  tuple val(file_id), path(bed)
+
+  output:
+  tuple val(file_id), path("*_extracted.fasta"), emit: fasta
+
+  script:
+"""
+bedtools getfasta ${params.fasta_from_bed} \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
+
+params.merge_bed = ""
+params.merge_bed_out = ""
+process merge_bed {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.merge_bed_out != "") {
+    publishDir "results/${params.merge_bed_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id), path(bed)
+
+  output:
+  tuple val(file_id), path("*_merged.fasta"), emit: bed
+
+  script:
+"""
+bedtools merge ${params.merge_bed} -i ${bed} > ${bed[0].simpleName}_merged.bed
+"""
+}
+
+params.bam_to_fastq_singleend = ""
+params.bam_to_fastq_singleend_out = ""
+process bam_to_fastq_singleend {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bam_id}"
+  if (params.bam_to_fastq_singleend_out != "") {
+    publishDir "results/${params.bam_to_fastq_singleend_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(bam_id), path(bam)
+
+  output:
+  tuple val(bam_id), path("*.fastq"), emit: fastq
+
+  script:
+"""
+bedtools bamtofastq \
+  ${params.bam_to_fastq_singleend} \
+  -i ${bam} -fq ${bam.baseName}.fastq
+"""
+}
+
+params.bam_to_fastq_pairedend = ""
+params.bam_to_fastq_pairedend_out = ""
+process bam_to_fastq_pairedend {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bam_id}"
+  if (params.bam_to_fastq_pairedend_out != "") {
+    publishDir "results/${params.bam_to_fastq_pairedend_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(bam_id), path(bam)
+
+  output:
+  tuple val(bam_id), path("*.fastq"), emit: fastq
+
+  script:
+"""
+bedtools bamtofastq \
+  ${params.bam_to_fastq_pairedend} \
+  -i ${bam} -fq ${bam.baseName}_R1.fastq -fq2 ${bam.baseName}_R2.fastq
+"""
+}
+
+params.bam_to_bedgraph = ""
+params.bam_to_bedgraph_out = ""
+process bam_to_bedgraph {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bam_id}"
+  if (params.bam_to_bedgraph_out != "") {
+    publishDir "results/${params.bam_to_bedgraph_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(bam_id), path(bam)
+
+  output:
+  tuple val(bam_id), path("*.bed"), emit: bed
+
+  script:
+"""
+bedtools genomecov \
+  ${params.bam_to_bedgraph} \
+  -ibam ${bam} \
+  -bg > ${bam.simpleName}.bed
+"""
+}

src/nf_modules/bioawk/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "1.0"
+container_url = "lbmc/bioawk:${version}"
+
+params.fasta_to_transcripts_lengths = ""
+params.fasta_to_transcripts_lengths_out = ""
+process fasta_to_transcripts_lengths {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.fasta_to_transcripts_lengths_out != "") {
+    publishDir "results/${params.fasta_to_transcripts_lengths_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fasta)
+
+  output:
+    tuple val(file_id), path("${fasta.simpleName}_transcripts_lengths.tsv"), emit: tsv
+
+  script:
+"""
+bioawk -c fastx '{print(\$name" "length(\$seq))}' ${fasta} > ${fasta.simpleName}_transcripts_lengths.tsv
+"""
+}
\ No newline at end of file

src/nf_modules/bioconvert/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.4.0"
+container_url = "lbmc/bioconvert:${version}"
+params.bigwig_to_wig = ""
+params.bigwig_to_wig_out = ""
+process bigwig_to_wig {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.bigwig_to_wig_out != "") {
+    publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id) path(bw)
+
+  output:
+  tuple val(file_id), path("*.wig"), emit: wig
+
+  script:
+"""
+bioconvert bigwig2wiggle ${bw} ${bw.simpleName}.wig
+"""
+}
+
+params.bigwig2_to_wig2 = ""
+params.bigwig2_to_wig2_out = ""
+process bigwig2_to_wig2 {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.bigwig_to_wig_out != "") {
+    publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id), path(bw_a), path(bw_b)
+
+  output:
+  tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig
+
+  script:
+"""
+bioconvert bigwig2wiggle ${bw_a} ${bw_a.simpleName}.wig
+bioconvert bigwig2wiggle ${bw_b} ${bw_b.simpleName}.wig
+"""
+}
\ No newline at end of file

src/nf_modules/bowtie/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "1.2.2"
+container_url = "lbmc/bowtie:${version}"
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${container_url}"
+  label "big_mem_multi_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("*.index*"), emit: index
+    tuple val(file_id), path("*_report.txt"), emit: report
+
+  script:
+"""
+bowtie-build --threads ${task.cpus} \
+  ${params.index_fasta} \
+  -f ${fasta} ${fasta.baseName}.index &> \
+  ${fasta.baseName}_bowtie_index_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_index_report.txt; then
+  exit 1
+fi
+"""
+}
+
+params.mapping_fastq = "--very-sensitive"
+params.mapping_fastq_out = ""
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+  if (params.mapping_fastq_out != "") {
+    publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(index_id), path(index)
+  tuple val(file_id), path(reads)
+
+  output:
+  tuple val(file_id), path("*.bam"), emit: bam
+  path "*_report.txt", emit: report
+
+  script:
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  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]
+    }
+  }
+  if (reads.size() == 2)
+  """
+  # -v specify the max number of missmatch, -k the number of match reported per
+  # reads
+  bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+    ${params.mapping_fastq} \
+    -1 ${reads[0]} -2 ${reads[1]} 2> \
+    ${file_id}_bowtie_report_tmp.txt | \
+    samtools view -Sb - > ${file_id}.bam
+
+  if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+    exit 1
+  fi
+  tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
+    ${file_id}_bowtie_mapping_report.txt
+  """
+  else
+  """
+  bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+    ${params.mapping_fastq}
+    -q ${reads} 2> \
+    ${file_id}_bowtie_report_tmp.txt | \
+    samtools view -Sb - > ${file_id}.bam
+
+  if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+    exit 1
+  fi
+  tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
+    ${file_id}_bowtie_mapping_report.txt
+  """
+}
+
+params.mapping_fastq_pairedend = ""
+process mapping_fastq_pairedend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+
+  input:
+  path index
+  tuple val(pair_id), path(reads)
+
+  output:
+  tuple val(pair_id), path("*.bam"), emit: bam
+  path "*_report.txt", emit: report
+
+  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]
+    }
+  }
+"""
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+  ${params.mapping_fastq_pairedend} \
+  -1 ${reads[0]} -2 ${reads[1]} 2> \
+  ${pair_id}_bowtie_report_tmp.txt | \
+  samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${pair_id}_bowtie_report_tmp.txt > \
+  ${pair_id}_bowtie_mapping_report.txt
+"""
+}
+
+params.mapping_fastq_singleend = ""
+process mapping_fastq_singleend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+  path index
+  tuple val(file_id), path(reads)
+
+  output:
+  set file_id, "*.bam", emit: bam
+  file "*_report.txt", emit: report
+
+  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]
+    }
+  }
+"""
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+  ${params.mapping_fastq_singleend} \
+  -q ${reads} 2> \
+  ${file_id}_bowtie_report_tmp.txt | \
+  samtools view -Sb - > ${file_id}.bam
+
+if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
+  ${file_id}_bowtie_mapping_report.txt
+"""
+}

src/nf_modules/bowtie2/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "2.3.4.1"
+container_url = "lbmc/bowtie2:${version}"
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${container_url}"
+  label "big_mem_multi_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("*.bt2"), emit: index
+    tuple val(file_id), path("*_report.txt"), emit: report
+
+  script:
+"""
+bowtie2-build --threads ${task.cpus} \
+  ${fasta} \
+  ${fasta.simpleName} &> \
+  ${fasta.simpleName}_bowtie2_index_report.txt
+
+if grep -q "Error" ${fasta.simpleName}_bowtie2_index_report.txt; then
+  exit 1
+fi
+"""
+}
+
+params.mapping_fastq = "--very-sensitive"
+params.mapping_fastq_out = ""
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.mapping_fastq_out != "") {
+    publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(index_id), path(index)
+  tuple val(file_id), path(reads)
+
+  output:
+  tuple val(file_id), path("*.bam"), emit: bam
+  path "*_report.txt", emit: report
+
+  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]
+    }
+  }
+  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
+  }
+
+  if (reads.size() == 2)
+  """
+  bowtie2 ${params.mapping_fastq} \
+    -p ${task.cpus} \
+    -x ${index_id} \
+    -1 ${reads[0]} \
+    -2 ${reads[1]} 2> \
+    ${file_prefix}_bowtie2_mapping_report_tmp.txt | \
+    samtools view -Sb - > ${file_prefix}.bam
+
+  if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
+    exit 1
+  fi
+  tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
+    ${file_prefix}_bowtie2_mapping_report.txt
+  """
+  else
+  """
+  bowtie2 ${params.mapping_fastq} \
+    -p ${task.cpus} \
+    -x ${index_id} \
+    -U ${reads} 2> \
+    ${file_prefix}_bowtie2_mapping_report_tmp.txt | \
+    samtools view -Sb - > ${file_prefix}.bam
+
+  if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
+    exit 1
+  fi
+  tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
+    ${file_prefix}_bowtie2_mapping_report.txt
+  """
+}

src/nf_modules/bwa/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.7.17"
+container_url = "lbmc/bwa:${version}"
+
+
+workflow mapping {
+  take:
+    fasta
+    fastq
+  main:
+    index_fasta(fasta)
+    mapping_fastq(index_fasta.out.index.collect(), fastq)
+  emit:
+    bam = mapping_fastq.out.bam
+    report = mapping_fastq.out.report
+}
+
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${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("${fasta.simpleName}.*"), emit: index
+    tuple val(file_id), path("*_bwa_report.txt"), emit: report
+
+  script:
+"""
+bwa index ${params.index_fasta} -p ${fasta.simpleName} ${fasta} \
+&> ${fasta.simpleName}_bwa_report.txt
+"""
+}
+
+
+params.mapping_fastq = ""
+params.mapping_fastq_out = ""
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.mapping_fastq_out != "") {
+    publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(index_id), path(index)
+  tuple val(file_id), path(reads)
+
+  output:
+  tuple val(file_id), path("*.bam"), emit: bam
+  tuple val(file_id), path("${file_prefix}_bwa_report.txt"), emit: report
+
+  script:
+  if (file_id instanceof List){
+    library = file_id[0]
+    file_prefix = file_id[0]
+  } else if (file_id instanceof Map) {
+      library = file_id[0]
+      file_prefix = file_id[0]
+      if (file_id.containsKey('library')) {
+        library = file_id.library
+        file_prefix = file_id.id
+      }
+  } else {
+    library = file_id
+    file_prefix = file_id
+  }
+bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
+  if (reads.size() == 2)
+"""
+bwa mem -t ${task.cpus} \
+${params.mapping_fastq} \
+-R '${bwa_mem_R}' \
+${index[0].baseName} ${reads[0]} ${reads[1]} 2> \
+  ${file_prefix}_bwa_report.txt | \
+  samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
+"""
+  else
+"""
+bwa mem -t ${task.cpus} \
+${params.mapping_fastq} \
+-R '${bwa_mem_R}' \
+${index[0].baseName} ${reads} 2> \
+  ${file_prefix}_bwa_report.txt | \
+  samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
+"""
+}
+

src/nf_modules/cellphonedb/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 = "mlepetit/cellphonedb:latest"
+
+params.cellphonedb = ""
+params.cellphonedb_out = ""
+params.pval=""
+params.thres=""
+params.iterations=""
+params.gene_id=""
+
+
+
+workflow cellphone_statistical_analysis {
+  take:
+    meta
+    counts
+
+  main:
+
+cpdb_methods_stats(meta,counts)
+cpdb_plot_dot_plot(cpdb_methods_stats.out.means,cpdb_methods_stats.out.pvalues)
+cpdb_plot_heatmap(cpdb_methods_stats.out.pvalues)
+
+
+  emit:
+    means = cpdb_methods_stats.out.means
+    pvalues = cpdb_methods_stats.out.pvalues
+    deconvoluted = cpdb_methods_stats.out.deconvoluted
+    significant_means = cpdb_methods_stats.out.significant_means
+    dot_plot = cpdb_plot_dot_plot.out.dot_plot
+    heatmap = cpdb_plot_heatmap.out.heatmap
+    heatmap_log = cpdb_plot_heatmap.out.heatmap_log
+    count_network = cpdb_plot_heatmap.out.count_network
+    interactions_count = cpdb_plot_heatmap.out.interactions_count
+
+
+}
+
+
+
+
+
+
+
+
+
+
+process cpdb_methods_stats {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(meta)
+    tuple val(id_mtx), path(counts)
+  
+  output:
+   tuple val(id_mtx), path("out/means.txt"), emit: means
+   tuple val(id_mtx), path("out/pvalues.txt"), emit: pvalues
+   tuple val(id_mtx), path("out/deconvoluted.txt"), emit: deconvoluted
+   tuple val(id_mtx), path("out/significant_means.txt"), emit: significant_means
+  
+script:
+  """
+cellphonedb method statistical_analysis ${params.meta} ${params.counts} --counts-data ${params.gene_id}  --threads ${task.cpus} --iterations ${params.iterations} --pvalue ${params.pval} --threshold ${params.thres}
+
+  """
+}
+
+
+process cpdb_plot_dot_plot {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(means)
+    tuple val(id_mtx), path(pvalues)
+
+  output:
+   tuple val(id_mtx), path("out/plot.pdf"), emit: dot_plot
+
+script:
+  """
+mkdir ./out
+cellphonedb plot dot_plot --means-path ${means} --pvalues-path ${pvalues} 
+
+  """
+}
+ 
+process cpdb_plot_heatmap {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(pvalues)
+
+  output:
+   tuple val(id_mtx), path("out/heatmap_count.pdf"), emit: heatmap
+ tuple val(id_mtx), path("out/heatmap_log_count.pdf"), emit: heatmap_log
+ tuple val(id_mtx), path("out/count_network.txt"), emit: count_network
+ tuple val(id_mtx), path("out/interaction_count.txt"), emit: interactions_count
+
+script:
+ 
+ """
+mkdir ./out
+cellphonedb plot heatmap_plot --pvalues-path ${pvalues} --pvalue ${params.pval} ${params.meta}
+
+  """
+}

src/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"
-      }
-    }
-  }
-}