From 2fda0df5d67a1c8204e1e98e8b3398dee19cab1c Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Mon, 23 Feb 2026 17:01:25 +0100
Subject: [PATCH 1/4] add bwa fastalign

---
 README.md               |  14 +++-
 aline.nf                | 115 +++++++++++++++++++++++++++++++--
 config/softwares.config |   3 +
 modules/bash.nf         |  55 +++++++++++++++-
 modules/bwafastalign.nf | 137 ++++++++++++++++++++++++++++++++++++++++
 5 files changed, 313 insertions(+), 11 deletions(-)
 create mode 100644 modules/bwafastalign.nf

diff --git a/README.md b/README.md
index 0e1d6a0..89b69e5 100644
--- a/README.md
+++ b/README.md
@@ -52,6 +52,9 @@ You can choose to run one or several aligner in parallel.
 | bowtie | ✅ | ✅ | ⚠️ | ⚠️ |
 | bowtie2 | ✅ | ✅ | ⚠️ | ⚠️ |
 | bwaaln | ✅ | ✅ R1 and R2 independently aligned then merged with bwa sampe | ⚠️ | ⚠️ |
+| bwafastalignaln | ✅ | ✅ R1 and R2 independently aligned then merged with bwa sampe | ⚠️ | ⚠️ |
+| bwafastalignmem | ✅ | ✅ | ✅ | ✅ |
+| bwafastalignsw | ✅ | ✅ | ⚠️ | ⚠️ |
 | bwamem | ✅ | ✅ | ✅ | ✅ |
 | bwamem2 | ✅ | ✅ | ✅ | ✅ |
 | bwasw | ✅ | ✅ | ⚠️ | ⚠️ |
@@ -88,6 +91,9 @@ It is then translated to the correct option in the following aligners:
 | bowtie | --fr / --rf / --ff |  ISF ISR IU / OSF OSR OU / MSF MSR MU| read orientation |
 | bowtie2 | --fr / --rf / --ff |  ISF ISR IU / OSF OSR OU / MSF MSR MU| read orientation |
 | bwaaln | 🚫 | 🚫 | 🚫 |
+| bwafastalignaln | 🚫 | 🚫 | 🚫 |
+| bwafastalignmem | 🚫 | 🚫 | 🚫 |
+| bwafastalignsw | 🚫 | 🚫 | 🚫 |
 | bwamem | 🚫 | 🚫 | 🚫 |
 | bwamem2 | 🚫 | 🚫 | 🚫 |
 | bwasw | 🚫 | 🚫 | 🚫 |
@@ -126,6 +132,9 @@ If you provide an annotation file the pipeline will pass automatically the file
 | bowtie | 🚫 |
 | bowtie2 | 🚫 |
 | bwaaln | 🚫 |
+| bwafastalignaln | 🚫 |
+| bwafastalignmem | 🚫 |
+| bwafastalignsw | 🚫 |
 | bwamem | 🚫 |
 | bwamem2 | 🚫 |
 | bwasw | 🚫 |
@@ -273,7 +282,7 @@ nextflow run Juke34/AliNe \
   --reads https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R1.fastq.gz \
   --reference https://raw.githubusercontent.com/Juke34/AliNe/refs/heads/main/test/yeast.fa \
   --read_type short_single \
-  --aligner bbmap,bowtie2,bwaaln,bwamem,bwasw,graphmap2,hisat2,minimap2,ngmlr,nucmer,star,subread,sublong \
+  --aligner bbmap,bowtie2,bwaaln,bwafastalignaln,bwafastalignmem,bwafastalignsw,bwamem,bwasw,graphmap2,hisat2,minimap2,ngmlr,nucmer,star,subread,sublong \
   --trimming_fastp \
   --fastqc \
   --samtools_stats \
@@ -337,7 +346,7 @@ 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, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
+        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwafastalign, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
         --outdir                    path to the output directory (default: alignment_results)
         --annotation                [Optional][used by graphmap2, STAR, subread] Absolute path to the annotation file (gtf or gff3)
 
@@ -364,6 +373,7 @@ On success you should get a message looking like this:
         --bowtie_options            additional options for bowtie
         --bowtie2_options           additional options for bowtie2
         --bwaaln_options            additional options for bwaaln
+        --bwafastalign_options      additional options for bwafastalign
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
diff --git a/aline.nf b/aline.nf
index 4294e5b..bc3da66 100644
--- a/aline.nf
+++ b/aline.nf
@@ -37,12 +37,15 @@ params.annotation = ""
 params.trimming_fastp = false
 
 // Aligner params
-align_tools = [ 'bbmap', 'bowtie', 'bowtie2', 'bwaaln', 'bwamem', 'bwamem2', 'bwasw', 'dragmap', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
+align_tools = [ 'bbmap', 'bowtie', 'bowtie2', 'bwaaln', 'bwamem', 'bwamem2', 'bwasw', 'bwafastalignaln','bwafastalignmem','bwafastalignsw', 'dragmap', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
 params.aligner = ''
 params.bbmap_options      = ''
 params.bowtie_options     = ''
 params.bowtie2_options    = ''
 params.bwaaln_options     = ''
+params.bwafastalignaln_options = ''
+params.bwafastalignmem_options = ''
+params.bwafastalignsw_options = ''
 params.bwamem_options     = ''
 params.bwamem2_options    = ''
 params.bwasw_options      = ''
@@ -270,6 +273,7 @@ include {bbmap_index; bbmap} from "$baseDir/modules/bbmap.nf"
 include {bowtie_index; bowtie} from "$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 {bwafastalign_index; bwafastalignaln; bwafastalignmem; bwafastalignsw} from "$baseDir/modules/bwafastalign.nf"
 include {bwamem2_index; bwamem2} from "$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"
@@ -277,7 +281,8 @@ 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 "$baseDir/modules/fastqc.nf"
 include {fastqc_ali as fastqc_ali_bbmap; fastqc_ali as fastqc_ali_bowtie ; fastqc_ali as fastqc_ali_bowtie2 ; 
-    fastqc_ali as fastqc_ali_bwaaln; fastqc_ali as fastqc_ali_bwamem; fastqc_ali as fastqc_ali_bwamem2; fastqc_ali as fastqc_ali_bwasw; fastqc_ali as fastqc_ali_dragmap; fastqc_ali as fastqc_ali_graphmap2 ; 
+    fastqc_ali as fastqc_ali_bwaaln; fastqc_ali as fastqc_ali_bwamem; fastqc_ali as fastqc_ali_bwamem2; fastqc_ali as fastqc_ali_bwasw; fastqc_ali as fastqc_ali_bwafastalignaln; 
+    fastqc_ali as fastqc_ali_bwafastalignmem;  fastqc_ali as fastqc_ali_bwafastalignsw; fastqc_ali as fastqc_ali_dragmap; fastqc_ali as fastqc_ali_graphmap2 ; 
     fastqc_ali as fastqc_ali_hisat2; fastqc_ali as fastqc_ali_kallisto; fastqc_ali as fastqc_ali_last; fastqc_ali as fastqc_ali_minimap2; fastqc_ali as fastqc_ali_ngmlr; 
     fastqc_ali as fastqc_ali_novoalign ; fastqc_ali as fastqc_ali_nucmer;  fastqc_ali as fastqc_ali_salmon; fastqc_ali as fastqc_ali_star; fastqc_ali as fastqc_ali_subread ; 
     fastqc_ali as fastqc_ali_sublong } from "$baseDir/modules/fastqc.nf"
@@ -294,25 +299,29 @@ 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; 
-         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_bwasw; samtools_sam2bam as samtools_sam2bam_bwafastalignaln;  samtools_sam2bam as samtools_sam2bam_bwafastalignmem; 
+         samtools_sam2bam as samtools_sam2bam_bwafastalignsw; 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_view_filter as samtools_view_filter_star; samtools_view_filter as samtools_view_filter_subread} from "$baseDir/modules/samtools.nf"
 include {samtools_sort as samtools_sort_bbmap; samtools_sort as samtools_sort_bowtie; samtools_sort as samtools_sort_bowtie2; samtools_sort as samtools_sort_bwaaln; 
-         samtools_sort as samtools_sort_bwamem; samtools_sort as samtools_sort_bwamem2; samtools_sort as samtools_sort_bwasw; samtools_sort as samtools_sort_dragmap; samtools_sort as samtools_sort_graphmap2; 
+         samtools_sort as samtools_sort_bwamem; samtools_sort as samtools_sort_bwamem2; samtools_sort as samtools_sort_bwasw; samtools_sort as samtools_sort_bwafastalignaln; 
+         samtools_sort as samtools_sort_bwafastalignmem; samtools_sort as samtools_sort_bwafastalignsw; samtools_sort as samtools_sort_dragmap; samtools_sort as samtools_sort_graphmap2; 
          samtools_sort as samtools_sort_hisat2; samtools_sort as samtools_sort_kallisto; samtools_sort as samtools_sort_last; samtools_sort as samtools_sort_minimap2; samtools_sort as samtools_sort_ngmlr; 
          samtools_sort as samtools_sort_novoalign;  samtools_sort as samtools_sort_nucmer; samtools_sort as samtools_sort_salmon;
          samtools_sort as samtools_sort_sublong; } from "$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_dragmap; 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_bwafastalignaln; samtools_stats as samtools_stats_ali_bwafastalignmem; 
+         samtools_stats as samtools_stats_ali_bwafastalignsw; 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_dragmap; 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_bwafastalignaln; 
+         samtools_index as samtools_index_bwafastalignmem; samtools_index as samtools_index_bwafastalignsw; 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"
@@ -886,7 +895,7 @@ workflow {
             }
         }
 
-        // ------------------- BWA ALN/MEM/SW -----------------
+        // ------------------- BWA ALN/MEM/SW/FASTALIGN -----------------
         if ("bwaaln" in aligner_list || "bwamem" in aligner_list || "bwasw" in aligner_list){
             // index
             bwa_index(reference.collect(), "alignment/bwa/indicies")
@@ -960,6 +969,80 @@ workflow {
                 }
             }
         }
+        // ------------------- BWAFASTALIGN ALN/MEM/SW/FASTALIGN -----------------
+        if ("bwafastalignaln" in aligner_list || "bwafastalignmem" in aligner_list || "bwafastalignsw" in aligner_list){
+            // index
+            bwafastalign_index(reference.collect(), "alignment/bwafastalign/indicies")
+            if ("bwafastalignaln" in aligner_list){
+                // align
+                bwafastalignaln(reads, reference.collect(), bwafastalign_index.out.collect(), "alignment/bwafastalign/bwafastalignaln") 
+                logs.concat(bwafastalignaln.out.bwafastalignaln_summary).set{logs} // save log
+                // convert sam to bam
+                samtools_sam2bam_bwafastalignaln(bwafastalignaln.out.tuple_sample_sam)
+                // sort and convert to cram
+                samtools_sort_bwafastalignaln(samtools_sam2bam_bwafastalignaln.out.tuple_sample_bam, reference.collect())
+                // index
+                samtools_index_bwafastalignaln(samtools_sort_bwafastalignaln.out, "alignment/bwafastalign/bwafastalignaln")
+                samtools_index_bwafastalignaln.out.tuple_sample_ali.set{bwafastalignaln_ali} // set name
+                // save aligned reads
+                sorted_ali.concat(bwafastalignaln_ali).set{sorted_ali} 
+                // stat on aligned reads
+                if(params.fastqc && !params.cram){
+                    fastqc_ali_bwafastalignaln(bwafastalignaln_ali, "fastqc/bwafastalignaln", "bwafastalignaln")
+                    logs.concat(fastqc_ali_bwafastalignaln.out).set{logs} // save log
+                }
+                if(params.samtools_stats){
+                    samtools_stats_ali_bwafastalignaln(bwafastalignaln_ali, reference.collect(), "samtools_stats/bwafastalignaln", "bwafastalignaln")
+                    logs.concat(samtools_stats_ali_bwafastalignaln.out).set{logs} // save log
+                }
+            }
+            if ("bwafastalignmem" in aligner_list){
+                // align
+                bwafastalignmem(reads, reference.collect(), bwafastalign_index.out.collect(), "alignment/bwafastalign/bwafastalignmem")
+                logs.concat(bwafastalignmem.out.bwafastalignmem_summary).set{logs} // save log
+                // convert sam to bam
+                samtools_sam2bam_bwafastalignmem(bwafastalignmem.out.tuple_sample_sam)
+                // sort and convert to cram
+                samtools_sort_bwafastalignmem(samtools_sam2bam_bwafastalignmem.out.tuple_sample_bam, reference.collect())
+                // index
+                samtools_index_bwafastalignmem(samtools_sort_bwafastalignmem.out, "alignment/bwafastalign/bwafastalignmem")
+                samtools_index_bwafastalignmem.out.tuple_sample_ali.set{bwafastalignmem_ali} // set name
+                // save aligned reads
+                sorted_ali.concat(bwafastalignmem_ali).set{sorted_ali} 
+                // stat on aligned reads
+                if(params.fastqc && !params.cram){
+                    fastqc_ali_bwafastalignmem(bwafastalignmem_ali, "fastqc/bwafastalignmem", "bwafastalignmem")
+                    logs.concat(fastqc_ali_bwafastalignmem.out).set{logs} // save log
+                }
+                if(params.samtools_stats){
+                    samtools_stats_ali_bwafastalignmem(bwafastalignmem_ali, reference.collect(), "samtools_stats/bwafastalignmem", "bwafastalignmem")
+                    logs.concat(samtools_stats_ali_bwafastalignmem.out).set{logs} // save log
+                }
+            }
+            if ("bwafastalignsw" in aligner_list){
+                // align
+                bwafastalignsw(reads, reference.collect(), bwafastalign_index.out.collect(), "alignment/bwafastalign/bwafastalignsw") 
+                logs.concat(bwafastalignsw.out.bwafastalignsw_summary).set{logs} // save log
+                // convert sam to bam
+                samtools_sam2bam_bwafastalignsw(bwafastalignsw.out.tuple_sample_sam)
+                // sort and convert to cram
+                samtools_sort_bwafastalignsw(samtools_sam2bam_bwafastalignsw.out.tuple_sample_bam, reference.collect())
+                // index
+                samtools_index_bwafastalignsw(samtools_sort_bwafastalignsw.out, "alignment/bwafastalign/bwafastalignsw")
+                samtools_index_bwafastalignsw.out.tuple_sample_ali.set{bwafastalignsw_ali} // set name
+                // save aligned reads
+                sorted_ali.concat(bwafastalignsw_ali).set{sorted_ali} 
+                // stat on aligned reads
+                if(params.fastqc && !params.cram){
+                    fastqc_ali_bwafastalignsw(bwafastalignsw_ali, "fastqc/bwafastalignsw", "bwafastalignsw")
+                    logs.concat(fastqc_ali_bwafastalignsw.out).set{logs} // save log
+                }
+                if(params.samtools_stats){
+                    samtools_stats_ali_bwafastalignsw(bwafastalignsw_ali, reference.collect(), "samtools_stats/bwafastalignsw", "bwafastalignsw")
+                    logs.concat(samtools_stats_ali_bwafastalignsw.out).set{logs} // save log
+                }
+            }
+        }
 
         // ------------------- BWA MEM2 -----------------
         if ("bwamem2" in aligner_list){
@@ -1451,6 +1534,9 @@ def helpMSG() {
         --bowtie_options            additional options for bowtie
         --bowtie2_options           additional options for bowtie2
         --bwaaln_options            additional options for bwaaln
+        --bwafastalignaln_options   additional options for bwafastalignaln
+        --bwafastalignmem_options   additional options for bwafastalignmem
+        --bwafastalignsw_options    additional options for bwafastalignsw
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
@@ -1517,6 +1603,21 @@ def printAlignerOptions(aligner_list) {
     bwasw parameters
         bwasw_options           : ${params.bwasw_options}
     """} 
+    if ("bwafastalignmem" in aligner_list){
+        sentence += """
+    bwafastalignmem parameters
+        bwafastalignmem_options    : ${params.bwafastalignmem_options}
+    """}
+    if ("bwafastalignaln" in aligner_list){
+        sentence += """
+    bwafastalignaln parameters
+        bwafastalignaln_options    : ${params.bwafastalignaln_options}
+    """} 
+    if ("bwafastalign" in aligner_list){
+        sentence += """
+    bwafastalignsw parameters
+        bwafastalignsw_options    : ${params.bwafastalignsw_options}
+    """} 
     if ("dragmap" in aligner_list){
         sentence += """
     dragmap parameters
diff --git a/config/softwares.config b/config/softwares.config
index 2b568cf..bbf72d6 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: 'bwafastalign' {
+        container = 'quay.io/biocontainers/bwa-fastalign:1.0.0--hb7acf71_0'
+    }
     withLabel: 'dragmap' {
         container = 'quay.io/biocontainers/dragmap:1.3.0--h5ca1c30_7'
     }
diff --git a/modules/bash.nf b/modules/bash.nf
index c84a985..dd30c62 100644
--- a/modules/bash.nf
+++ b/modules/bash.nf
@@ -66,20 +66,30 @@ process check_aligner{
             }
         }
         
+        // --- bwa fastalign aln tool ---
+        if ( "bwafastalignaln" in aligner_list ){
+            if ( meta.read_type == "pacbio" || meta.read_type == "ont"){
+                log.info "${meta.uid} => Bwafastalignaln aligner is not recommended to align long reads!"
+            }
+        }
 
         // --- bwa mem tool ---
         if ( "bwamem" in aligner_list ){
             // short and long reads ok
         }
 
+        // --- bwa fastalign mem tool ---
+        if ( "bwafastalignmem" in aligner_list ){
+            // short and long reads ok
+        }
+
         // --- bwa mem2 tool ---
         if ("bwamem2" in aligner_list ){
             if ( meta.read_type == "pacbio" || meta.read_type == "ont"){
                 log.info "${meta.uid} => Bwamem2 aligner is not recommended to align long reads!"
             }
         }
-       
-
+    
         // --- bwa sw tool ---
         if ( "bwasw" in aligner_list ){
             if (meta.read_type == "pacbio" || meta.read_type == "ont"){
@@ -87,6 +97,13 @@ process check_aligner{
             }
         }
 
+        // --- bwa fastalign sw tool ---
+        if ( "bwafastalignsw" in aligner_list ){
+            if (meta.read_type == "pacbio" || meta.read_type == "ont"){
+                log.info "${meta.uid} => Bwafastalignsw aligner is not recommended to align long reads!"
+            }
+        }
+
         // --- dragmap tool ---
         if ( "dragmap" in aligner_list ){
             if (meta.read_type == "pacbio" || meta.read_type == "ont"){
@@ -336,6 +353,40 @@ process check_aligner_params{
             meta.bwasw_options = bwasw_options
         }
 
+        // --- bwa fastalign aln tool ---
+        if ( "bwafastalignaln" in aligner_list ){
+            def bwafastalignaln_options = params.bwafastalignaln_options ?: ""
+            meta.bwafastalignaln_options = bwafastalignaln_options
+        }
+
+        // --- bwa fastalign mem tool ---
+        if ( "bwafastalignmem" in aligner_list ){
+            def bwafastalignmem_options = params.bwafastalignmem_options ?: ""
+            if( !params.relax ){
+                if (meta.read_type == "pacbio"){
+                    if ( ! bwafastalignmem_options.contains(" pacbio") ){
+                        bwafastalignmem_options += " -x pacbio"
+                        log.info "${meta.uid} => Pacbio reads being used, setting -x pacbio to bwafastalignmem!\n" +
+                                 "    However, if you know what you are doing you can activate the AliNe --relax parameter and avoid this behavior."
+                    }
+                }
+                if (meta.read_type == "ont"){
+                    if ( ! bwafastalignmem_options.contains(" ont2d") ){
+                        bwafastalignmem_options += " -x ont2d"
+                        log.info "${meta.uid} => Ont reads being used, setting -x ont2d to bwafastalignmem!\n" + 
+                                 "    However, if you know what you are doing you can activate the AliNe --relax parameter and avoid this behavior."
+                    }
+                }
+            }
+            meta.bwafastalignmem_options = bwafastalignmem_options
+        }
+
+        // --- bwa fastalign sw tool ---
+        if ( "bwafastalignsw" in aligner_list ){
+            def bwafastalignsw_options = params.bwafastalignsw_options ?: ""
+            meta.bwafastalignsw_options = bwafastalignsw_options
+        }
+
         // --- dragmap tool ---
         if ( "dragmap" in aligner_list ){
             def dragmap_options = params.dragmap_options ?: ""
diff --git a/modules/bwafastalign.nf b/modules/bwafastalign.nf
new file mode 100644
index 0000000..201c3e5
--- /dev/null
+++ b/modules/bwafastalign.nf
@@ -0,0 +1,137 @@
+/*
+* To align with BWA-fastalign
+* The index used must be the basename of the genome reference file
+*/
+
+process bwafastalign_index {
+    label 'bwafastalign'
+    tag "$genome_fasta"
+    publishDir "${params.outdir}/${outpath}", mode: 'copy'
+
+    input:
+        path(genome_fasta)
+        val outpath
+
+    output:
+        path("*")
+
+    script:
+        """
+        bwa-fastalign index $genome_fasta -p ${genome_fasta.baseName}
+        """
+}
+
+/*
+* To align with BWA FASTALIGN ALN
+* The index used must be the basename of the genome reference file
+*/
+process bwafastalignaln {
+    label 'bwafastalign'
+    tag "${meta.uid}"
+    publishDir "${params.outdir}/${outpath}", pattern: "*_sam.log", mode: 'copy'
+
+    input:
+        tuple val(meta), path(reads)
+        path genome
+        path bwafastalign_index_files
+        val outpath
+
+    output:
+        tuple val(meta), path ("*.sam"), emit: tuple_sample_sam
+        path "*_sam.log",  emit: bwafastalignaln_summary
+
+    script:
+        // options for bwafastalign-aln
+        def bwafastalignaln_options = meta.bwafastalignaln_options ?: ""
+
+        // catch output file prefix 
+        def fileName = meta.uid + meta.suffix + "_bwafastalignaln"
+
+        if (meta.paired){
+        """
+            bwa-fastalign aln ${bwafastalignaln_options} -t ${task.cpus} ${genome.baseName} ${reads[0]} > ${reads[0].baseName}_r1.sai 2> ${reads[0].baseName}_r1_sai.log 
+            bwa-fastalign aln ${bwafastalignaln_options} -t ${task.cpus} ${genome.baseName} ${reads[1]} > ${reads[1].baseName}_r2.sai 2> ${reads[1].baseName}_r2_sai.log
+            bwa-fastalign sampe ${genome.baseName}  ${reads[0].baseName}_r1.sai ${reads[1].baseName}_r2.sai ${reads[0]} ${reads[1]} > ${fileName}.sam 2> ${fileName}_sam.log 
+   
+        """
+        } else {
+        """
+            bwa-fastalign aln ${bwafastalignaln_options} -t ${task.cpus} ${genome.baseName} ${reads} > ${fileName}.sai 2> ${fileName}_sai.log 
+            bwa-fastalign samse ${genome.baseName}  ${fileName}.sai ${reads} > ${fileName}.sam 2> ${fileName}_sam.log 
+        """
+        }
+}
+
+/*
+* To align with BWA FASTALIGN MEM
+* The index used must be the basename of the genome reference file
+*/
+process bwafastalignmem {
+    label 'bwafastalign'
+    tag "${meta.uid}"
+    publishDir "${params.outdir}/${outpath}", pattern: "*bwafastalign.log", mode: 'copy'
+
+    input:
+        tuple val(meta), path(reads)
+        path genome
+        path bwafastalign_index_files
+        val outpath
+
+    output:
+        tuple val(meta), path ("*.sam"), emit: tuple_sample_sam
+        path "*.log",  emit: bwafastalignmem_summary
+
+    script:
+        // options for bwafastalign-mem
+        def bwafastalignmem_options = meta.bwafastalignmem_options ?: ""
+
+        // catch output file prefix 
+        def fileName = meta.uid + meta.suffix + "_bwafastalignmem"
+      
+        if (meta.paired){
+            """
+            bwa-fastalign mem ${bwafastalignmem_options} -t ${task.cpus} ${genome.baseName} ${reads[0]} ${reads[1]} > ${fileName}.sam 2> ${fileName}.log 
+            """
+        } else {
+            """
+            bwa-fastalign mem ${bwafastalignmem_options} -t ${task.cpus} ${genome.baseName} ${reads} > ${fileName}.sam 2> ${fileName}.log 
+            """
+        }
+}
+
+/*
+* To align with BWA FASTALIGN MEM
+* The index used must be the basename of the genome reference file
+*/
+process bwafastalignsw {
+    label 'bwafastalign'
+    tag "${meta.uid}"
+    publishDir "${params.outdir}/${outpath}", pattern: "*.log", mode: 'copy'
+
+    input:
+        tuple val(meta), path(reads)
+        path genome
+        path bwafastalign_index_files
+        val outpath
+
+    output:
+        tuple val(meta), path ("*.sam"), emit: tuple_sample_sam
+        path "*.log",  emit: bwafastalignsw_summary
+
+    script:
+        // options for bwafastalign-mem
+        def bwafastalignsw_options = meta.bwafastalignsw_options ?: ""
+
+        // catch output file prefix 
+        def fileName = meta.uid + meta.suffix + "_bwafastalignsw"
+
+        if (meta.paired){
+            """
+            bwa-fastalign bwasw ${bwafastalignsw_options} -t ${task.cpus} ${genome.baseName} ${reads[0]} ${reads[1]} > ${fileName}.sam 2> ${fileName}.log 
+            """
+        } else {
+            """
+            bwa-fastalign bwasw ${bwafastalignsw_options} -t ${task.cpus} ${genome.baseName} ${reads} > ${fileName}.sam 2> ${fileName}.log 
+            """
+        }
+}
\ No newline at end of file

From f80a3c77e7230183e17f61422d3fb3c2c98df1f7 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Tue, 24 Feb 2026 08:44:24 +0100
Subject: [PATCH 2/4] add test in CI

---
 .github/workflows/main.yml | 2 ++
 README.md                  | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9bf9c36..e79dffa 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -57,6 +57,8 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
       # Run tests sequentialy
+      - name: test short single_fastalign
+        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --aligner bwafastalignaln,bwafastalignmem,bwafastalignsw
       - name: test short single
         run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf
       - name: test short single cram
diff --git a/README.md b/README.md
index 89b69e5..72fabd2 100644
--- a/README.md
+++ b/README.md
@@ -373,7 +373,9 @@ On success you should get a message looking like this:
         --bowtie_options            additional options for bowtie
         --bowtie2_options           additional options for bowtie2
         --bwaaln_options            additional options for bwaaln
-        --bwafastalign_options      additional options for bwafastalign
+        --bwafastalignaln_options   additional options for bwafastalignaln
+        --bwafastalignmem_options   additional options for bwafastalignmem
+        --bwafastalignsw_options    additional options for bwafastalignsw
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw

From 7503b4d474174cafa666db6357b0586ae594534a Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@gmail.com>
Date: Tue, 24 Feb 2026 09:40:37 +0100
Subject: [PATCH 3/4] Update test command to use bwafastalignmem only

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e79dffa..c549157 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -58,7 +58,7 @@ jobs:
       - uses: actions/checkout@v3
       # Run tests sequentialy
       - name: test short single_fastalign
-        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --aligner bwafastalignaln,bwafastalignmem,bwafastalignsw
+        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --aligner bwafastalignmem
       - name: test short single
         run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf
       - name: test short single cram
@@ -72,4 +72,4 @@ jobs:
       - name: test csv
         run: nextflow run -ansi-log -profile docker,test_csv aline.nf
       - name: test remote
-        run: nextflow run -ansi-log -profile docker,test_remote aline.nf
\ No newline at end of file
+        run: nextflow run -ansi-log -profile docker,test_remote aline.nf

From e5ef6f5c62aa812282b23b62599970e58108f55f Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Wed, 25 Feb 2026 11:02:02 +0100
Subject: [PATCH 4/4] use of bwafastalignmem onlyn sw and aln seems to be bug
 https://github.com/zzhofict/BWA-FastAlign/issues/6

---
 .github/workflows/main.yml           |  2 --
 README.md                            | 10 +---------
 aline.nf                             |  4 +---
 profiles/test_illumina_single.config |  2 +-
 4 files changed, 3 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e79dffa..9bf9c36 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -57,8 +57,6 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
       # Run tests sequentialy
-      - name: test short single_fastalign
-        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --aligner bwafastalignaln,bwafastalignmem,bwafastalignsw
       - name: test short single
         run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf
       - name: test short single cram
diff --git a/README.md b/README.md
index 72fabd2..1e3cc60 100644
--- a/README.md
+++ b/README.md
@@ -52,9 +52,7 @@ You can choose to run one or several aligner in parallel.
 | bowtie | ✅ | ✅ | ⚠️ | ⚠️ |
 | bowtie2 | ✅ | ✅ | ⚠️ | ⚠️ |
 | bwaaln | ✅ | ✅ R1 and R2 independently aligned then merged with bwa sampe | ⚠️ | ⚠️ |
-| bwafastalignaln | ✅ | ✅ R1 and R2 independently aligned then merged with bwa sampe | ⚠️ | ⚠️ |
 | bwafastalignmem | ✅ | ✅ | ✅ | ✅ |
-| bwafastalignsw | ✅ | ✅ | ⚠️ | ⚠️ |
 | bwamem | ✅ | ✅ | ✅ | ✅ |
 | bwamem2 | ✅ | ✅ | ✅ | ✅ |
 | bwasw | ✅ | ✅ | ⚠️ | ⚠️ |
@@ -91,9 +89,7 @@ It is then translated to the correct option in the following aligners:
 | bowtie | --fr / --rf / --ff |  ISF ISR IU / OSF OSR OU / MSF MSR MU| read orientation |
 | bowtie2 | --fr / --rf / --ff |  ISF ISR IU / OSF OSR OU / MSF MSR MU| read orientation |
 | bwaaln | 🚫 | 🚫 | 🚫 |
-| bwafastalignaln | 🚫 | 🚫 | 🚫 |
 | bwafastalignmem | 🚫 | 🚫 | 🚫 |
-| bwafastalignsw | 🚫 | 🚫 | 🚫 |
 | bwamem | 🚫 | 🚫 | 🚫 |
 | bwamem2 | 🚫 | 🚫 | 🚫 |
 | bwasw | 🚫 | 🚫 | 🚫 |
@@ -132,9 +128,7 @@ If you provide an annotation file the pipeline will pass automatically the file
 | bowtie | 🚫 |
 | bowtie2 | 🚫 |
 | bwaaln | 🚫 |
-| bwafastalignaln | 🚫 |
 | bwafastalignmem | 🚫 |
-| bwafastalignsw | 🚫 |
 | bwamem | 🚫 |
 | bwamem2 | 🚫 |
 | bwasw | 🚫 |
@@ -346,7 +340,7 @@ 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, bwafastalign, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
+        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwafastalignmem, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
         --outdir                    path to the output directory (default: alignment_results)
         --annotation                [Optional][used by graphmap2, STAR, subread] Absolute path to the annotation file (gtf or gff3)
 
@@ -373,9 +367,7 @@ On success you should get a message looking like this:
         --bowtie_options            additional options for bowtie
         --bowtie2_options           additional options for bowtie2
         --bwaaln_options            additional options for bwaaln
-        --bwafastalignaln_options   additional options for bwafastalignaln
         --bwafastalignmem_options   additional options for bwafastalignmem
-        --bwafastalignsw_options    additional options for bwafastalignsw
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
diff --git a/aline.nf b/aline.nf
index bc3da66..d574dac 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', 'bwafastalignaln','bwafastalignmem','bwafastalignsw', 'dragmap', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
+align_tools = [ 'bbmap', 'bowtie', 'bowtie2', 'bwaaln', 'bwamem', 'bwamem2', 'bwasw', 'bwafastalignmem', 'dragmap', 'graphmap2', 'hisat2', 'kallisto', 'last', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'salmon', 'star', 'subread', 'sublong' ]
 params.aligner = ''
 params.bbmap_options      = ''
 params.bowtie_options     = ''
@@ -1534,9 +1534,7 @@ def helpMSG() {
         --bowtie_options            additional options for bowtie
         --bowtie2_options           additional options for bowtie2
         --bwaaln_options            additional options for bwaaln
-        --bwafastalignaln_options   additional options for bwafastalignaln
         --bwafastalignmem_options   additional options for bwafastalignmem
-        --bwafastalignsw_options    additional options for bwafastalignsw
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
diff --git a/profiles/test_illumina_single.config b/profiles/test_illumina_single.config
index a947ca1..d486bd2 100644
--- a/profiles/test_illumina_single.config
+++ b/profiles/test_illumina_single.config
@@ -11,7 +11,7 @@ params {
     annotation = "$baseDir/test/yeast.gtf"
     data_type = "RNA"
     read_type = "short_single"
-    aligner = 'bbmap,bowtie,bowtie2,bwaaln,bwamem,bwamem2,bwasw,graphmap2,hisat2,kallisto,last,minimap2,ngmlr,nucmer,salmon,star,subread,sublong'
+    aligner = 'bbmap,bowtie,bowtie2,bwaaln,bwamem,bwafastalignmem,bwamem2,bwasw,graphmap2,hisat2,kallisto,last,minimap2,ngmlr,nucmer,salmon,star,subread,sublong'
     trimming_fastp = true
     fastqc = true
     samtools_stats = true