From 05ef1e0c6549a6ae2579b1c6157572a533f88446 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 13:11:05 +0100
Subject: [PATCH 1/6] add dragmap fix #39

---
 README.md                      |  5 +++-
 aline.nf                       | 47 +++++++++++++++++++++++++++++-----
 config/ressources/hpc.config   |  4 +++
 config/ressources/local.config |  4 +++
 config/softwares.config        |  3 +++
 modules/bash.nf                | 13 ++++++++++
 6 files changed, 69 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index d6979a5..573ede1 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,7 @@ It is then translated to the correct option in the following aligners:
 | bwamem | 🚫 | 🚫 | 🚫 |
 | bwamem2 | 🚫 | 🚫 | 🚫 |
 | bwasw | 🚫 | 🚫 | 🚫 |
+| dragmap | 🚫 | 🚫 | 🚫 |
 | graphmap2 | 🚫 | 🚫 | 🚫 |
 | hisat2 | --rna-strandness [ F / R / FR / RF ] | SF / SR / ISF OSF MSF / ISR OSR MSR | strand information |
 | hisat2 | --fr / --rf / --ff | I / O / M | read orientation |
@@ -128,6 +129,7 @@ If you provide an annotation file the pipeline will pass automatically the file
 | bwamem | 🚫 |
 | bwamem2 | 🚫 |
 | bwasw | 🚫 |
+| dragmap | 🚫 |
 | graphmap2 | GTF (--gtf)  |
 | hisat2 | 🚫 |
 | kallisto | 🚫 |
@@ -335,7 +337,7 @@ On success you should get a message looking like this:
                                         control1,path/to/data1.fastq.gz,,auto,short_single,rna
                                         control2,path/to/data2_R1.fastq.gz,path/to/data2_R2.fastq.gz,auto,short_paired,rna
         --reference                 path to the reference file (fa, fa.gz, fasta or fasta.gz)
-        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwamem, bwamem2, bwasw, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, star, subread, sublong]
+        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
         --outdir                    path to the output directory (default: alignment_results)
         --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files.
         --annotation                [Optional][used by graphmap2, STAR, subread] Absolute path to the annotation file (gtf or gff3)
@@ -364,6 +366,7 @@ On success you should get a message looking like this:
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
+        --dragmap_options           additional options for dragmap
         --graphmap2_options         additional options for graphmap2
         --hisat2_options            additional options for hisat2
         --kallisto_options          additional options for kallisto
diff --git a/aline.nf b/aline.nf
index 9dc6514..5af1ce2 100644
--- a/aline.nf
+++ b/aline.nf
@@ -37,7 +37,7 @@ params.annotation = ""
 params.trimming_fastp = false
 
 // Aligner params
-align_tools = [ 'bbmap', 'bowtie', 'bowtie2', 'bwaaln', 'bwamem', 'bwamem2', 'bwasw', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
+align_tools = [ 'bbmap', 'bowtie', 'bowtie2', 'bwaaln', 'bwamem', 'bwamem2', 'bwasw', 'dragmap', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
 params.aligner = ''
 params.bbmap_options      = ''
 params.bowtie_options     = ''
@@ -46,6 +46,7 @@ params.bwaaln_options     = ''
 params.bwamem_options     = ''
 params.bwamem2_options    = ''
 params.bwasw_options      = ''
+params.dragmap_options    = ''
 params.graphmap2_options  = '' // owler option is possible
 params.hisat2_options     = ''
 params.kallisto_options   = ''
@@ -268,12 +269,13 @@ include {bowtie_index; bowtie} from "$baseDir/modules/bowtie.nf"
 include {bowtie2_index; bowtie2} from "$baseDir/modules/bowtie2.nf"
 include {bwa_index; bwaaln; bwamem; bwasw} from "$baseDir/modules/bwa.nf"
 include {bwamem2_index; bwamem2} from "$baseDir/modules/bwamem2.nf"
+include {dragmap_index; dragmap} from "$baseDir/modules/dragmap.nf"
 include {seqkit_convert; seqkit_clean_fasta_headers} from "$baseDir/modules/seqkit.nf"
 include {graphmap2_index; graphmap2} from "$baseDir/modules/graphmap2.nf"
 include {fastp} from "$baseDir/modules/fastp.nf"
 include {fastqc as fastqc_raw; fastqc as fastqc_fastp} from "$baseDir/modules/fastqc.nf"
 include {fastqc_ali as fastqc_ali_bbmap; fastqc_ali as fastqc_ali_bowtie ; fastqc_ali as fastqc_ali_bowtie2 ; 
-    fastqc_ali as fastqc_ali_bwaaln; fastqc_ali as fastqc_ali_bwamem; fastqc_ali as fastqc_ali_bwamem2; fastqc_ali as fastqc_ali_bwasw; fastqc_ali as fastqc_ali_graphmap2 ; 
+    fastqc_ali as fastqc_ali_bwaaln; fastqc_ali as fastqc_ali_bwamem; fastqc_ali as fastqc_ali_bwamem2; fastqc_ali as fastqc_ali_bwasw; fastqc_ali as fastqc_ali_dragmap; fastqc_ali as fastqc_ali_graphmap2 ; 
     fastqc_ali as fastqc_ali_hisat2; fastqc_ali as fastqc_ali_kallisto; fastqc_ali as fastqc_ali_last; fastqc_ali as fastqc_ali_minimap2; fastqc_ali as fastqc_ali_ngmlr; 
     fastqc_ali as fastqc_ali_novoalign ; fastqc_ali as fastqc_ali_nucmer;  fastqc_ali as fastqc_ali_salmon; fastqc_ali as fastqc_ali_star; fastqc_ali as fastqc_ali_subread ; 
     fastqc_ali as fastqc_ali_sublong } from "$baseDir/modules/fastqc.nf"
@@ -289,24 +291,24 @@ include {fasta_uncompress} from "$baseDir/modules/pigz.nf"
 include {salmon_index; salmon_guess_lib; salmon} from "$baseDir/modules/salmon.nf" 
 include {samtools_sam2bam_nucmer; samtools_sam2bam as samtools_sam2bam_bowtie; samtools_sam2bam as samtools_sam2bam_bowtie2; 
          samtools_sam2bam as samtools_sam2bam_bwaaln; samtools_sam2bam as samtools_sam2bam_bwamem; samtools_sam2bam as samtools_sam2bam_bwamem2; 
-         samtools_sam2bam as samtools_sam2bam_bwasw; samtools_sam2bam as samtools_sam2bam_graphmap2; samtools_sam2bam as samtools_sam2bam_hisat2;
+         samtools_sam2bam as samtools_sam2bam_bwasw; samtools_sam2bam as samtools_sam2bam_dragmap; samtools_sam2bam as samtools_sam2bam_graphmap2; samtools_sam2bam as samtools_sam2bam_hisat2;
          samtools_sam2bam as samtools_sam2bam_last; samtools_sam2bam as samtools_sam2bam_minimap2; 
          samtools_sam2bam as samtools_sam2bam_ngmlr; samtools_sam2bam as samtools_sam2bam_novoalign; samtools_sam2bam as samtools_sam2bam_salmon } from "$baseDir/modules/samtools.nf"
 include {samtools_bam2cram as samtools_bam2cram_star; samtools_bam2cram as samtools_bam2cram_subread} from "$baseDir/modules/samtools.nf"
 include {samtools_sort as samtools_sort_bbmap; samtools_sort as samtools_sort_bowtie; samtools_sort as samtools_sort_bowtie2; samtools_sort as samtools_sort_bwaaln; 
-         samtools_sort as samtools_sort_bwamem; samtools_sort as samtools_sort_bwamem2; samtools_sort as samtools_sort_bwasw; samtools_sort as samtools_sort_graphmap2; 
+         samtools_sort as samtools_sort_bwamem; samtools_sort as samtools_sort_bwamem2; samtools_sort as samtools_sort_bwasw; samtools_sort as samtools_sort_dragmap; samtools_sort as samtools_sort_graphmap2; 
          samtools_sort as samtools_sort_hisat2; samtools_sort as samtools_sort_kallisto; samtools_sort as samtools_sort_last; samtools_sort as samtools_sort_minimap2; samtools_sort as samtools_sort_ngmlr; 
          samtools_sort as samtools_sort_novoalign;  samtools_sort as samtools_sort_nucmer; samtools_sort as samtools_sort_salmon;
          samtools_sort as samtools_sort_sublong; } from "$baseDir/modules/samtools.nf"
 include {samtools_stats as samtools_stats_ali_bbmap; samtools_stats as samtools_stats_ali_bowtie; samtools_stats as samtools_stats_ali_bowtie2 ;
          samtools_stats as samtools_stats_ali_bwaaln; samtools_stats as samtools_stats_ali_bwamem; samtools_stats as samtools_stats_ali_bwamem2;
-         samtools_stats as samtools_stats_ali_bwasw; samtools_stats as samtools_stats_ali_graphmap2; samtools_stats as samtools_stats_ali_hisat2; 
+         samtools_stats as samtools_stats_ali_bwasw; samtools_stats as samtools_stats_ali_dragmap; samtools_stats as samtools_stats_ali_graphmap2; samtools_stats as samtools_stats_ali_hisat2; 
          samtools_stats as samtools_stats_ali_kallisto; samtools_stats as samtools_stats_ali_last; samtools_stats as samtools_stats_ali_minimap2; samtools_stats as samtools_stats_ali_ngmlr; 
          samtools_stats as samtools_stats_ali_novoalign ; samtools_stats as samtools_stats_ali_nucmer; samtools_stats as samtools_stats_ali_salmon; samtools_stats as samtools_stats_ali_star; 
          samtools_stats as samtools_stats_ali_subread; samtools_stats as samtools_stats_ali_sublong } from "$baseDir/modules/samtools.nf"
 include {samtools_merge_bam_if_paired} from "$baseDir/modules/samtools.nf"
 include {samtools_index as samtools_index_bbmap; samtools_index as samtools_index_bowtie; samtools_index as samtools_index_bowtie2; samtools_index as samtools_index_bwaaln;
-         samtools_index as samtools_index_bwamem; samtools_index as samtools_index_bwamem2; samtools_index as samtools_index_bwasw; samtools_index as samtools_index_graphmap2;
+         samtools_index as samtools_index_bwamem; samtools_index as samtools_index_bwamem2; samtools_index as samtools_index_bwasw; samtools_index as samtools_index_dragmap; samtools_index as samtools_index_graphmap2;
          samtools_index as samtools_index_hisat2; samtools_index as samtools_index_kallisto; samtools_index as samtools_index_last; samtools_index as samtools_index_minimap2;
          samtools_index as samtools_index_ngmlr; samtools_index as samtools_index_novoalign; samtools_index as samtools_index_nucmer; samtools_index as samtools_index_salmon;
          samtools_index as samtools_index_star; samtools_index as samtools_index_subread; samtools_index as samtools_index_sublong} from "$baseDir/modules/samtools.nf"
@@ -969,6 +971,33 @@ workflow {
             }
         }
 
+        // ------------------- DRAGMAP -----------------
+        if ("dragmap" in aligner_list){
+            // index
+            dragmap_index(reference.collect(), "alignment/dragmap/indicies")
+            // align
+            dragmap(reads, reference.collect(), dragmap_index.out.collect(), "alignment/dragmap")
+            logs.concat(dragmap.out.dragmap_summary).set{logs} // save log
+            // convert sam to bam
+            samtools_sam2bam_dragmap(dragmap.out.tuple_sample_sam)
+            // sort and convert to cram
+            samtools_sort_dragmap(samtools_sam2bam_dragmap.out.tuple_sample_bam, reference.collect())
+            // index
+            samtools_index_dragmap(samtools_sort_dragmap.out, "alignment/dragmap")
+            samtools_index_dragmap.out.tuple_sample_ali.set{dragmap_ali} // set name
+            // save aligned reads
+            sorted_ali.concat(dragmap_ali).set{sorted_ali} 
+            // stat on aligned reads
+            if(params.fastqc && !params.cram){
+                fastqc_ali_dragmap(dragmap_ali, "fastqc/dragmap", "dragmap")
+                logs.concat(fastqc_ali_dragmap.out).set{logs} // save log
+            }
+            if(params.samtools_stats){
+                samtools_stats_ali_dragmap(dragmap_ali, reference.collect(), "samtools_stats/dragmap", "dragmap")
+                logs.concat(samtools_stats_ali_dragmap.out).set{logs} // save log
+            }
+        }
+
         // ------------------- GRAPHMAP2 -----------------
         if ("graphmap2" in aligner_list ){
             // index
@@ -1395,6 +1424,7 @@ def helpMSG() {
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
+        --dragmap_options           additional options for dragmap
         --graphmap2_options         additional options for graphmap2
         --hisat2_options            additional options for hisat2
         --kallisto_options          additional options for kallisto
@@ -1457,6 +1487,11 @@ def printAlignerOptions(aligner_list) {
     bwasw parameters
         bwasw_options           : ${params.bwasw_options}
     """} 
+    if ("dragmap" in aligner_list){
+        sentence += """
+    dragmap parameters
+        dragmap_options         : ${params.dragmap_options}
+    """} 
     if ("graphmap2" in aligner_list){
         sentence += """
     graphmap2 parameters
diff --git a/config/ressources/hpc.config b/config/ressources/hpc.config
index 00288d7..6501a86 100644
--- a/config/ressources/hpc.config
+++ b/config/ressources/hpc.config
@@ -25,6 +25,10 @@ process {
         cpus = 16
         time = '4h'
     }
+    withLabel: 'dragmap' {
+        cpus = 16
+        time = '4h'
+    }
     withName: 'fastp' {
         cpus = 16
         time = '2h'
diff --git a/config/ressources/local.config b/config/ressources/local.config
index b1458c3..910bfd8 100644
--- a/config/ressources/local.config
+++ b/config/ressources/local.config
@@ -25,6 +25,10 @@ process {
         cpus = 2
         time = '4h'
     }
+    withLabel: 'dragmap' {
+        cpus = 2
+        time = '4h'
+    }
     withName: 'fastp' {
         cpus = 2
         time = '2h'
diff --git a/config/softwares.config b/config/softwares.config
index d8a2e16..8b9d460 100644
--- a/config/softwares.config
+++ b/config/softwares.config
@@ -17,6 +17,9 @@ process {
     withLabel: 'bwamem2' {
         container = 'quay.io/biocontainers/bwa-mem2:2.2.1--he70b90d_8'
     }
+    withLabel: 'dragmap' {
+        container = 'quay.io/biocontainers/dragmap:1.3.0--h5ca1c30_7'
+    }
     withLabel: 'fastp' {
         container = 'quay.io/biocontainers/fastp:0.23.4--h125f33a_5'
     }
diff --git a/modules/bash.nf b/modules/bash.nf
index c8d9860..f83a6d4 100644
--- a/modules/bash.nf
+++ b/modules/bash.nf
@@ -87,6 +87,13 @@ process check_aligner{
             }
         }
 
+        // --- dragmap tool ---
+        if ( "dragmap" in aligner_list ){
+            if (meta.read_type == "pacbio" || meta.read_type == "ont"){
+                log.info "${meta.id} => Dragmap aligner is not recommended to align long reads!"
+            }
+        }
+
         // --- graphmap2 tool ---
         if ( "graphmap2" in aligner_list ){
             if ( meta.read_type == "short_single" && meta.read_type == "short_paired"){
@@ -329,6 +336,12 @@ process check_aligner_params{
             meta.bwasw_options = bwasw_options
         }
 
+        // --- dragmap tool ---
+        if ( "dragmap" in aligner_list ){
+            def dragmap_options = params.dragmap_options ?: ""
+            meta.dragmap_options = dragmap_options
+        }
+
         // --- graphmap2 tool ---
         if ( "graphmap2" in aligner_list ){
             def graphmap2_options = params.graphmap2_options ?: ""

From 5812ac8b3d00925a13c03953ddfe8c5f030ebd4f Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 13:11:48 +0100
Subject: [PATCH 2/6] publish indicies only if salmon mapping asked (salmon is
 used to detect strandeness in all cases)

---
 modules/salmon.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/salmon.nf b/modules/salmon.nf
index 72bb98f..be6b336 100644
--- a/modules/salmon.nf
+++ b/modules/salmon.nf
@@ -6,7 +6,7 @@ https://github.com/COMBINE-lab/salmon
 process salmon_index {
     label 'salmon'
     tag "$genome_fasta"
-    publishDir "${params.outdir}/${outpath}", mode: 'copy'
+    publishDir "${params.outdir}/${outpath}", mode: 'copy', enabled: params.aligner.contains('salmon')
 
     input:
         path genome_fasta

From 7c16515f64a5afcea2c0bfdde9fe17ab2db6375b Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 13:12:16 +0100
Subject: [PATCH 3/6] add dragmap module

---
 modules/dragmap.nf | 67 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 modules/dragmap.nf

diff --git a/modules/dragmap.nf b/modules/dragmap.nf
new file mode 100644
index 0000000..d98b985
--- /dev/null
+++ b/modules/dragmap.nf
@@ -0,0 +1,67 @@
+/* Module related to dragmap
+https://github.com/Illumina/DRAGMAP
+
+info:
+DRAGEN-GATK is a software-only implementation of Illumina's DRAGEN mapper 
+that is freely available and open source. It provides the same accuracy and 
+functionality as the FPGA-based DRAGEN Bio-IT Platform, but runs on general 
+purpose CPUs.
+*/ 
+
+/*
+* To index with DRAGMAP
+*/
+process dragmap_index {
+    label 'dragmap'
+    tag "$genome_fasta"
+    publishDir "${params.outdir}/${outpath}", mode: 'copy'
+
+    input:
+        path(genome_fasta)
+        val outpath
+
+    output:
+        path("dragmap_index")
+
+    script:
+        """
+        mkdir -p dragmap_index
+        dragen-os --build-hash-table true --ht-reference ${genome_fasta} --output-directory dragmap_index
+        """
+}
+
+/*
+* To align with DRAGMAP
+*/
+process dragmap {
+    label 'dragmap'
+    tag "${meta.id}"
+    publishDir "${params.outdir}/${outpath}", pattern: "*dragmap.log", mode: 'copy'
+
+    input:
+        tuple val(meta), path(reads)
+        path genome
+        path dragmap_index
+        val outpath
+
+    output:
+        tuple val(meta), path ("*dragmap.sam"), emit: tuple_sample_sam
+        path "*dragmap.log",  emit: dragmap_summary
+
+    script:
+        // options for dragmap
+        def dragmap_options = meta.dragmap_options ?: ""
+
+        // catch filename
+        def fileName =  AlineUtils.getCleanName(reads)
+      
+        if (meta.paired){
+            """
+            dragen-os ${dragmap_options} --num-threads ${task.cpus} -r dragmap_index -1 ${reads[0]} -2 ${reads[1]} > ${fileName}_dragmap.sam 2> ${fileName}_dragmap.log 
+            """
+        } else {
+            """
+            dragen-os ${dragmap_options} --num-threads ${task.cpus} -r dragmap_index -1 ${reads} > ${fileName}_dragmap.sam 2> ${fileName}_dragmap.log 
+            """
+        }
+}

From 79d49a90ed53b2d7cd3a8940c990639875fee762 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 13:45:41 +0100
Subject: [PATCH 4/6] add filter_unmapped option to reduce output size wheen
 needed

---
 .github/workflows/main.yml |  2 +-
 README.md                  |  3 ++-
 aline.nf                   | 18 ++++++++++++--
 modules/samtools.nf        | 51 ++++++++++++++++++++++++++++++++------
 4 files changed, 62 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 569d505..9bf9c36 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -60,7 +60,7 @@ jobs:
       - name: test short single
         run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf
       - name: test short single cram
-        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --cram
+        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --cram --filter_unmapped
       - name: test short paired
         run: nextflow run -ansi-log -profile docker,test_illumina_paired aline.nf
       - name: test ont
diff --git a/README.md b/README.md
index 573ede1..cdd2e53 100644
--- a/README.md
+++ b/README.md
@@ -339,7 +339,6 @@ On success you should get a message looking like this:
         --reference                 path to the reference file (fa, fa.gz, fasta or fasta.gz)
         --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
         --outdir                    path to the output directory (default: alignment_results)
-        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files.
         --annotation                [Optional][used by graphmap2, STAR, subread] Absolute path to the annotation file (gtf or gff3)
 
     Type of input reads
@@ -356,6 +355,8 @@ On success you should get a message looking like this:
         --trimming_fastp            run fastp for trimming (default: false)
         --fastqc                    run fastqc on raw and aligned reads (default: false). Note: FastQC will be automatically disabled for alignment files when --cram is enabled.
         --samtools_stats            run samtools stats on aligned reads (default: false)
+        --filter_unmapped           filter out unmapped reads from final alignment files (default: false). Filtering is performed during sorting when possible for optimal performance.
+        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files. Conversion is performed during sorting when possible for optimal performance.
         --multiqc_config            path to the multiqc config file (default: config/multiqc_conf.yml)
 
     Aligner specific options
diff --git a/aline.nf b/aline.nf
index 5af1ce2..3ca8438 100644
--- a/aline.nf
+++ b/aline.nf
@@ -72,6 +72,7 @@ params.fastqc = false
 params.samtools_stats = false
 params.multiqc_config = "$baseDir/config/multiqc_conf.yml"
 params.cram = false
+params.filter_unmapped = false
 
 // other
 params.help = null
@@ -248,10 +249,11 @@ Extra step paramesters
     trimming_fastp              : ${params.trimming_fastp}
     fastqc                      : ${params.fastqc}
     samtools_stats              : ${params.samtools_stats}
+    cram                        : ${params.cram}
+    filter_unmapped             : ${params.filter_unmapped}
 
 Report Parameters
     multiqc_config              : ${params.multiqc_config}
-    cram                        : ${params.cram}
 
 Aligner Parameters (provided by user)
 """
@@ -295,6 +297,7 @@ include {samtools_sam2bam_nucmer; samtools_sam2bam as samtools_sam2bam_bowtie; s
          samtools_sam2bam as samtools_sam2bam_last; samtools_sam2bam as samtools_sam2bam_minimap2; 
          samtools_sam2bam as samtools_sam2bam_ngmlr; samtools_sam2bam as samtools_sam2bam_novoalign; samtools_sam2bam as samtools_sam2bam_salmon } from "$baseDir/modules/samtools.nf"
 include {samtools_bam2cram as samtools_bam2cram_star; samtools_bam2cram as samtools_bam2cram_subread} from "$baseDir/modules/samtools.nf"
+include {samtools_view_filter as samtools_view_filter_star; samtools_view_filter as samtools_view_filter_subread} from "$baseDir/modules/samtools.nf"
 include {samtools_sort as samtools_sort_bbmap; samtools_sort as samtools_sort_bowtie; samtools_sort as samtools_sort_bowtie2; samtools_sort as samtools_sort_bwaaln; 
          samtools_sort as samtools_sort_bwamem; samtools_sort as samtools_sort_bwamem2; samtools_sort as samtools_sort_bwasw; samtools_sort as samtools_sort_dragmap; samtools_sort as samtools_sort_graphmap2; 
          samtools_sort as samtools_sort_hisat2; samtools_sort as samtools_sort_kallisto; samtools_sort as samtools_sort_last; samtools_sort as samtools_sort_minimap2; samtools_sort as samtools_sort_ngmlr; 
@@ -1254,6 +1257,11 @@ workflow {
             } else {
                 star.out.tuple_sample_bam.set{star_ali} // save aligned reads
             }
+            // filter unmapped reads if requested
+            if(params.filter_unmapped){
+                samtools_view_filter_star(star_ali)
+                samtools_view_filter_star.out.tuple_sample_bam.set{star_ali}
+            }
             // convert to cram if requested
             if(params.cram){
                 samtools_bam2cram_star(star_ali, reference.collect())
@@ -1282,6 +1290,11 @@ workflow {
             // align
             subread(reads, reference.collect(), subread_index.out.collect(), annotation.collect(), "alignment/subread")
             subread.out.tuple_sample_bam.set{subread_ali} // set name
+            // filter unmapped reads if requested
+            if(params.filter_unmapped){
+                samtools_view_filter_subread(subread_ali)
+                samtools_view_filter_subread.out.tuple_sample_bam.set{subread_ali}
+            }
             // convert to cram if requested
             if(params.cram){
                 samtools_bam2cram_subread(subread_ali, reference.collect())
@@ -1397,7 +1410,6 @@ def helpMSG() {
         --reference                 path to the reference file (fa, fa.gz, fasta or fasta.gz)
         --aligner                   aligner(s) to use among this list (comma or space separated) ${align_tools}
         --outdir                    path to the output directory (default: alignment_results)
-        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files.
         --annotation                [Optional][used by STAR, Tophat2] Absolute path to the annotation file (gtf or gff3)
 
     Type of input reads
@@ -1414,6 +1426,8 @@ def helpMSG() {
         --trimming_fastp            run fastp for trimming (default: false)
         --fastqc                    run fastqc on raw and aligned reads (default: false). Note: FastQC will be automatically disabled for alignment files when --cram is enabled.
         --samtools_stats            run samtools stats on aligned reads (default: false)
+        --filter_unmapped           filter out unmapped reads from final alignment files (default: false). Filtering is performed during sorting when possible for optimal performance.
+        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files. Conversion is performed during sorting when possible for optimal performance.
         --multiqc_config            path to the multiqc config file (default: config/multiqc_conf.yml)
 
     Aligner specific options
diff --git a/modules/samtools.nf b/modules/samtools.nf
index d94f9af..04b116c 100644
--- a/modules/samtools.nf
+++ b/modules/samtools.nf
@@ -84,22 +84,37 @@ process samtools_sort {
         tuple val(meta), path ("*_sorted.{bam,cram}"), emit: tuple_sample_ali
 
     script:
+        
+        // catch filename
+        def extension = params.filter_unmapped ? "_filtered_sorted" : "_sorted"
+        filename = AlineUtils.getCleanName(bam) + extension
 
         if (params.cram) {
-            """
-                samtools sort -@ ${task.cpus} --reference ${genome_fasta} -o ${bam.baseName}_sorted.cram ${bam}
-            """
+            if (params.filter_unmapped) {
+                """
+                    samtools view -b -F 4 -@ ${task.cpus} ${bam} | samtools sort -@ ${task.cpus} --reference ${genome_fasta} -o ${filename}.cram -
+                """
+            } else {
+                """
+                    samtools sort -@ ${task.cpus} --reference ${genome_fasta} -o ${filename}.cram ${bam}
+                """
+            }
         } else {
-            """
-                samtools sort -@ ${task.cpus} -o ${bam.baseName}_sorted.bam ${bam}
-            """
+            if (params.filter_unmapped) {
+                """
+                    samtools view -b -F 4 -@ ${task.cpus} ${bam} | samtools sort -@ ${task.cpus} -o ${filename}.bam -
+                """
+            } else {
+                """
+                    samtools sort -@ ${task.cpus} -o ${filename}.bam ${bam}
+                """
+            }
         }
 }
 
-
 /*
 http://www.htslib.org/doc/samtools-view.html
-Convert BAM to CRAM format
+Convert BAM to CRAM format (done during sorting when possible for optimal performance, otherwise as a separate step)
 */
 process samtools_bam2cram {
     label 'samtools'
@@ -142,6 +157,26 @@ process samtools_index {
         """
 }
 
+/*
+http://www.htslib.org/doc/samtools-view.html
+Filter unmapped reads from BAM file (done during sorting when possible for optimal performance, otherwise as a separate step)
+*/
+process samtools_view_filter {
+    label 'samtools'
+    tag "${meta.id}"
+
+    input:
+        tuple val(meta), path(bam)
+
+    output:
+        tuple val(meta), path ("*_filtered.bam"), emit: tuple_sample_bam
+
+    script:
+        """
+            samtools view -b -F 4 -@ ${task.cpus} -o ${bam.baseName}_filtered.bam ${bam}
+        """
+}
+
 /*
 http://www.htslib.org/doc/samtools-stats.html
 Produces comprehensive statistics from alignment file

From d57fe96d5d345ff5e7d68e933b3bffff81245833 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 15:13:35 +0100
Subject: [PATCH 5/6] generate the tsv comparison table at the end
 automatically (when stat available)

---
 README.md                            |  50 +------------
 aline.nf                             |   4 +
 bin/r_rendering.R                    | 106 +++++++++++++++++++++++++++
 config/multiqc_conf.yml              |   8 ++
 config/softwares.config              |   3 +
 modules/r.nf                         |  15 ++++
 nextflow.config                      |   2 +-
 profiles/test_illumina_paired.config |   2 +-
 8 files changed, 141 insertions(+), 49 deletions(-)
 create mode 100755 bin/r_rendering.R
 create mode 100644 modules/r.nf

diff --git a/README.md b/README.md
index cdd2e53..0e1d6a0 100644
--- a/README.md
+++ b/README.md
@@ -456,7 +456,8 @@ Here the description of typical ouput you will get from AliNe:
     │
     └── MultiQC                                               # MultiQC folder that aggregate results across many samples into a single report
         ├── multiqc_report.html                               # Report with interactive plots for statistics across many samples.
-        └── multiqc_report_data                               # Plot and data used by the multiqc_report.html
+        ├── multiqc_report_data                               # Plot and data used by the multiqc_report.html
+        └── alignment_comparison.tsv                          # A tsv table summerizing the statistics of the different aligners across all samples.
 ```
 
 ### Statistics
@@ -501,52 +502,7 @@ Some information produced via FastQC or Samtools stats are reported at the top o
 
 <img src="img/multiqc.png" />
 
-In order to facilitate the reading of this `General Statistics` you can export the table in tsv using the `Export as CSV...` button and execute the following piece of R code on the downloaded `general_stats_table.tsv` file :
-
-```R
-# install packages
-install.packages("dplyr")
-install.packages("stringr")
-install.packages("tidyr")
-install.packages("knitr")
-
-# Load necessary libraries
-library(dplyr)
-library(stringr)
-library(tidyr)
-library(knitr)
-
-# Read the TSV file
-file_path <- "general_stats_table.tsv"
-df <- read.delim(file_path, check.names = FALSE)
-
-# clean sample name to remove suffix _*_samtoolsstats
-df$Sample <- df$Sample |> stringr::str_remove_all("_\\d+_samtoolsstats")
-
-# sample name as row name
-rownames(df) <- df$Sample
-
-# remove Sample column and clean up the column names
-tableout <- cbind(ID = rownames(df), stack(df[-1])) |> 
-  transform(ind = as.character(ind) |> stringr::str_remove_all("\\.\\d+"))
-
-# remove na values
-tableout <- tableout[!is.na(tableout$values),]
-# remove . values
-tableout$values <- tableout$values |> stringr::str_remove_all("^\\.$")
-
-# pivot data
-tableout <- tableout |> pivot_wider(id_cols = ID , names_from = ind, values_from = values, 
-              values_fn = \(x) paste(unique(x), collapse = ""))
-
-# round each value to 4 decimals
-tableout <- tableout |> mutate(across(-ID, ~round(as.numeric(.), 4)))
-
-# print with nice output
-knitr::kable(tableout)
-```
-
-You will get a table similar to this one:  
+To make the General Statistics easier to read and compare, AliNe also generates a TSV file named `alignment_comparison.tsv`, located in the `<output_directory>/MultiQC` directory. This file contains the same information as the `General Statistics` table, but in a simpler, tabular format that is more convenient for comparisons. It looks like this:  
 
 ```
 |ID                                  |    Dups| GC|   Seqs| Error rate| Non-primary| Reads mapped| % Mapped| Total seqs|
diff --git a/aline.nf b/aline.nf
index 3ca8438..0ba780e 100644
--- a/aline.nf
+++ b/aline.nf
@@ -290,6 +290,7 @@ include {ngmlr} from "$baseDir/modules/ngmlr.nf"
 include {nucmer} from "$baseDir/modules/mummer4.nf"
 include {novoalign_index; novoalign} from "$baseDir/modules/novoalign.nf"
 include {fasta_uncompress} from "$baseDir/modules/pigz.nf"
+include {r_rendering} from "$baseDir/modules/r.nf"
 include {salmon_index; salmon_guess_lib; salmon} from "$baseDir/modules/salmon.nf" 
 include {samtools_sam2bam_nucmer; samtools_sam2bam as samtools_sam2bam_bowtie; samtools_sam2bam as samtools_sam2bam_bowtie2; 
          samtools_sam2bam as samtools_sam2bam_bwaaln; samtools_sam2bam as samtools_sam2bam_bwamem; samtools_sam2bam as samtools_sam2bam_bwamem2; 
@@ -1346,6 +1347,9 @@ workflow {
         // ------------------- MULTIQC -----------------
         multiqc(logs.collect(),params.multiqc_config)
 
+        // ------------------- R rendering -----------------
+        r_rendering(multiqc.out.multiqc_report_data)
+
     emit:
         sorted_ali                // channel: [ val(meta), path(alignment), path(index) ]
 
diff --git a/bin/r_rendering.R b/bin/r_rendering.R
new file mode 100755
index 0000000..6ab0dfa
--- /dev/null
+++ b/bin/r_rendering.R
@@ -0,0 +1,106 @@
+#!/usr/bin/env Rscript
+
+# Load necessary libraries
+suppressPackageStartupMessages({
+  library(dplyr)
+  library(stringr)
+  library(tidyr)
+  library(knitr)
+})
+
+# Parse command-line arguments manually
+args <- commandArgs(trailingOnly = TRUE)
+
+# Function to display help
+show_help <- function() {
+  cat("Process and format MultiQC general stats table\n\n")
+  cat("Usage: r_rendering.R -i INPUT [-o OUTPUT] [-f FORMAT]\n\n")
+  cat("Options:\n")
+  cat("  -i, --input FILE    Input TSV file path (required)\n")
+  cat("  -o, --output FILE   Output file path (optional, prints to stdout if not specified)\n")
+  cat("  -f, --format FORMAT Output format: 'tsv' or 'markdown' [default: tsv]\n")
+  cat("  -h, --help          Show this help message\n\n")
+  quit(save = "no", status = 0)
+}
+
+# Initialize options with defaults
+opt <- list(input = NULL, output = NULL, format = "tsv")
+
+# Parse arguments
+i <- 1
+while (i <= length(args)) {
+  arg <- args[i]
+  if (arg %in% c("-h", "--help")) {
+    show_help()
+  } else if (arg %in% c("-i", "--input")) {
+    opt$input <- args[i + 1]
+    i <- i + 1
+  } else if (arg %in% c("-o", "--output")) {
+    opt$output <- args[i + 1]
+    i <- i + 1
+  } else if (arg %in% c("-f", "--format")) {
+    opt$format <- args[i + 1]
+    i <- i + 1
+  }
+  i <- i + 1
+}
+
+# Check if input file is provided and exists
+if (is.null(opt$input)) {
+  cat("Error: Input file is required\n\n")
+  show_help()
+}
+
+if (!file.exists(opt$input)) {
+  stop(sprintf("Error: Input file '%s' not found", opt$input))
+}
+
+# Read the TSV file
+df <- read.delim(opt$input, check.names = FALSE)
+
+# Clean column names: extract metric name after last dash
+# samtools_stats_bbmap_stats-error_rate -> error_rate
+colnames(df)[-1] <- colnames(df)[-1] |> 
+  stringr::str_extract("[^-]+$")
+
+# clean sample name to remove suffix _*_samtoolsstats
+df$Sample <- df$Sample |> stringr::str_remove_all("_\\d+_samtoolsstats")
+
+# sample name as row name
+rownames(df) <- df$Sample
+
+# remove Sample column and clean up the column names
+tableout <- cbind(ID = rownames(df), stack(df[-1])) |> 
+  transform(ind = as.character(ind) |> stringr::str_remove_all("\\.\\d+"))
+
+# remove na values
+tableout <- tableout[!is.na(tableout$values),]
+# remove . values
+tableout$values <- tableout$values |> stringr::str_remove_all("^\\.$")
+
+# pivot data
+tableout <- tableout |> pivot_wider(id_cols = ID , names_from = ind, values_from = values, 
+              values_fn = \(x) paste(unique(x), collapse = ""))
+
+# round each value to 4 decimals
+tableout <- tableout |> mutate(across(-ID, ~round(as.numeric(.), 4)))
+
+# Output results
+if (tolower(opt$format) == "markdown") {
+  # Markdown format
+  if (!is.null(opt$output)) {
+    output_table <- knitr::kable(tableout, format = "markdown", align = 'r')
+    writeLines(output_table, con = opt$output)
+    cat(sprintf("Output written to: %s\n", opt$output))
+  } else {
+    cat(knitr::kable(tableout, format = "markdown", align = 'r'), sep = "\n")
+  }
+} else {
+  # TSV format (default)
+  if (!is.null(opt$output)) {
+    write.table(tableout, file = opt$output, sep = "\t", quote = FALSE, row.names = FALSE)
+    cat(sprintf("Output written to: %s\n", opt$output))
+  } else {
+    write.table(tableout, file = stdout(), sep = "\t", quote = FALSE, row.names = FALSE)
+  }
+}
\ No newline at end of file
diff --git a/config/multiqc_conf.yml b/config/multiqc_conf.yml
index b467add..8484232 100644
--- a/config/multiqc_conf.yml
+++ b/config/multiqc_conf.yml
@@ -72,6 +72,14 @@ module_order:
         name: "Samtools stats (bwasw)"
         path_filters:
           - "*bwasw_*.txt"
+    - fastqc:
+        name: "FastQC (dragmap)"
+        path_filters:
+          - "*dragmap_logs/*"
+    - samtools:
+        name: "Samtools stats (dragmap)"
+        path_filters:
+          - "*dragmap_*.txt"
     - fastqc:
         name: "FastQC (graphmap2)"
         path_filters:
diff --git a/config/softwares.config b/config/softwares.config
index 8b9d460..2b568cf 100644
--- a/config/softwares.config
+++ b/config/softwares.config
@@ -57,6 +57,9 @@ process {
     withLabel: 'pigz' {
         container = 'quay.io/biocontainers/pigz:2.8'
   	}
+    withLabel: 'r_rendering' {
+        container = 'rocker/tidyverse'
+  	}
     withLabel: 'salmon' {
         container = 'quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2'
     }
diff --git a/modules/r.nf b/modules/r.nf
new file mode 100644
index 0000000..777ad93
--- /dev/null
+++ b/modules/r.nf
@@ -0,0 +1,15 @@
+process r_rendering {
+    label 'r_rendering'
+    publishDir "${params.outdir}/MultiQC", mode: 'copy'
+
+    input:
+        path multiqc_data_dir
+
+    output:
+        path "alignment_comparison.tsv", emit: comparison_table_tsv
+
+    script:
+        """
+        r_rendering.R -i ${multiqc_data_dir}/multiqc_general_stats.txt -o alignment_comparison.tsv
+        """
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index c5eee0f..90346ee 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
     description = 'Nextflow alignment pipeline'
     mainScript = 'aline.nf'
     nextflowVersion = '>=22.04.0'
-    version = '1.5.3'
+    version = '1.6.0'
 }
 
 
diff --git a/profiles/test_illumina_paired.config b/profiles/test_illumina_paired.config
index cfb63ab..125de5a 100644
--- a/profiles/test_illumina_paired.config
+++ b/profiles/test_illumina_paired.config
@@ -11,7 +11,7 @@ params {
     read_type = "short_paired"
     reference = "$baseDir/test/yeast.fa"
     annotation = "$baseDir/test/yeast.gtf"
-    aligner = 'bbmap,bowtie,bowtie2,bwaaln,bwamem,bwamem2,bwasw,graphmap2,hisat2,last,minimap2,ngmlr,nucmer,salmon,star,subread,sublong'
+    aligner = 'bbmap,bowtie,bowtie2,bwaaln,bwamem,bwamem2,bwasw,dragmap,graphmap2,hisat2,last,minimap2,ngmlr,nucmer,salmon,star,subread,sublong'
     star_options = "--genomeSAindexNbases 9" // the default 14 is too large for the genome size=1351857
     multiqc_config = "$baseDir/config/multiqc_conf.yml"
 }
\ No newline at end of file

From 0c9a4aad982758d39886867452657c1895cc3741 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 5 Feb 2026 15:25:17 +0100
Subject: [PATCH 6/6] add label

---
 config/ressources/hpc.config   | 4 ++++
 config/ressources/local.config | 4 ++++
 modules/multiqc.nf             | 4 ++--
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/config/ressources/hpc.config b/config/ressources/hpc.config
index 6501a86..9af56ab 100644
--- a/config/ressources/hpc.config
+++ b/config/ressources/hpc.config
@@ -69,6 +69,10 @@ process {
         cpus = 16
         time = '4h'
     }
+    withLabel: 'r_rendering' {
+        cpus = 1
+        time = '1h'
+    }
     withLabel: 'salmon' {
         cpus = 16
         time = '4h'
diff --git a/config/ressources/local.config b/config/ressources/local.config
index 910bfd8..d969827 100644
--- a/config/ressources/local.config
+++ b/config/ressources/local.config
@@ -69,6 +69,10 @@ process {
         cpus = 2
         time = '4h'
     }
+    withLabel: 'r_rendering' {
+        cpus = 1
+        time = '1h'
+    }
     withLabel: 'salmon' {
         cpus = 2
         time = '4h'
diff --git a/modules/multiqc.nf b/modules/multiqc.nf
index cd9a4df..f4dcfa8 100644
--- a/modules/multiqc.nf
+++ b/modules/multiqc.nf
@@ -7,8 +7,8 @@ process multiqc {
         path multiqc_config
 
     output:
-        path "*multiqc_report.html", optional:true
-        path "*_data", optional:true
+        path "*multiqc_report.html", optional:true, emit: multiqc_report_html
+        path "*_data", optional:true, emit: multiqc_report_data
 
     script:
         """