nf-core · afonsoguerra · Jan 24, 2026
diff --git a/docs/output.md b/docs/output.md
@@ -271,19 +271,19 @@ The files in the alignment folder have the following base name structure:
   - `QC/`
     - `alignments/`: alignments to assemblies
       - `<SampleName>_<stage>.bam` Alignment
-      - `<SampleName>_<stage>.bai` bam index file
+      - `<SampleName>_<stage>.csi` bam index file
       - `<SampleName>_<stage>.stats` comprehensive statistics from alignment file
       - `<SampleName>_<stage>.idxstats` alignment summary statistics
       - `<SampleName>_<stage>.flagstat` number of alignments for each FLAG type
       - `shortreads/`: folder containing short read mapping for pilon
         - `<SampleName>_shortreads.bam` Alignment
-        - `<SampleName>_shortreads.bai` bam index file
+        - `<SampleName>_shortreads.csi` bam index file
         - `<SampleName>_shortreads.stats` comprehensive statistics from alignment file
         - `<SampleName>_shortreads.idxstats` alignment summary statistics
         - `<SampleName>_shortreads.flagstat` number of alignments for each FLAG type
       - `reference/`: folder containing alignment of long reads to reference
         - `<SampleName>_to_reference.bam` Alignment
-        - `<SampleName>_to_reference.bai` bam index file
+        - `<SampleName>_to_reference.csi` bam index file
         - `<SampleName>_to_reference.stats` comprehensive statistics from alignment file
         - `<SampleName>_to_reference.idxstats` alignment summary statistics
         - `<SampleName>_to_reference.flagstat` number of alignments for each FLAG type

diff --git a/modules/nf-core/pilon/main.nf b/modules/nf-core/pilon/main.nf
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
diff --git a/subworkflows/local/assemble/main.nf b/subworkflows/local/assemble/main.nf
@@ -158,7 +158,7 @@ workflow ASSEMBLE {
     */
     if (params.skip_alignments) {
         // Sample sheet layout when skipping assembly and mapping
-        // sample,ontreads,assembly,ref_fasta,ref_gff,assembly_bam,assembly_bai,ref_bam
+        // sample,ontreads,assembly,ref_fasta,ref_gff,assembly_bam,assembly_csi,ref_bam
         ch_input
             .map { row -> [row.meta, row.ref_bam] }
             .set { ch_ref_bam }

diff --git a/subworkflows/local/bam_sort_stat/main.nf b/subworkflows/local/bam_sort_stat/main.nf
@@ -21,12 +21,12 @@ workflow BAM_INDEX_STATS_SAMTOOLS {
 
     SAMTOOLS_INDEX(bam)
 
-    BAM_STATS_SAMTOOLS(bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), fasta)
+    BAM_STATS_SAMTOOLS(bam.join(SAMTOOLS_INDEX.out.csi, by: [0]), fasta)
 
     versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions).mix(BAM_STATS_SAMTOOLS.out.versions)
 
     emit:
-    bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ]
+    csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ]
     stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ]
     flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]

diff --git a/subworkflows/local/mapping/map_sr/main.nf b/subworkflows/local/mapping/map_sr/main.nf
@@ -14,33 +14,33 @@ workflow MAP_SR {
         .join(genome_assembly)
         .set { map_assembly }
 
-    ALIGN_SHORT(map_assembly, true, 'bai', false, false)
+    ALIGN_SHORT(map_assembly, true, 'csi', false, false)
 
     versions = ch_versions.mix(ALIGN_SHORT.out.versions)
 
     ALIGN_SHORT.out.bam.set { aln_to_assembly_bam }
 
-    ALIGN_SHORT.out.index.set { aln_to_assembly_bai }
+    ALIGN_SHORT.out.index.set { aln_to_assembly_csi }
 
     aln_to_assembly_bam
-        .join(aln_to_assembly_bai)
-        .set { aln_to_assembly_bam_bai }
+        .join(aln_to_assembly_csi)
+        .set { aln_to_assembly_bam_csi }
 
     map_assembly
         .map { meta, _reads, fasta -> [ meta, fasta ] }
         .set { ch_fasta }
 
-    BAM_STATS(aln_to_assembly_bam_bai, ch_fasta)
+    BAM_STATS(aln_to_assembly_bam_csi, ch_fasta)
 
     versions = ch_versions.mix(BAM_STATS.out.versions)
 
     aln_to_assembly_bam
-        .join(aln_to_assembly_bai)
-        .set { aln_to_assembly_bam_bai }
+        .join(aln_to_assembly_csi)
+        .set { aln_to_assembly_bam_csi }
 
     emit:
     aln_to_assembly_bam
-    aln_to_assembly_bai
-    aln_to_assembly_bam_bai
+    aln_to_assembly_csi
+    aln_to_assembly_bam_csi
     versions
 }
diff --git a/subworkflows/local/mapping/map_to_assembly/main.nf b/subworkflows/local/mapping/map_to_assembly/main.nf
@@ -13,20 +13,20 @@ workflow MAP_TO_ASSEMBLY {
         .join(genome_assembly)
         .set { map_assembly }
 
-    ALIGN(map_assembly, true, 'bai', false, false)
+    ALIGN(map_assembly, true, 'csi', false, false)
 
     ALIGN.out.bam.set { aln_to_assembly_bam }
-    ALIGN.out.index.set { aln_to_assembly_bai }
+    ALIGN.out.index.set { aln_to_assembly_csi }
 
     map_assembly
         .map { meta, _reads, fasta -> [meta, fasta] }
         .set { ch_fasta }
 
     aln_to_assembly_bam
-        .join(aln_to_assembly_bai)
-        .set { aln_to_assembly_bam_bai }
+        .join(aln_to_assembly_csi)
+        .set { aln_to_assembly_bam_csi }
 
-    BAM_STATS(aln_to_assembly_bam_bai, ch_fasta )
+    BAM_STATS(aln_to_assembly_bam_csi, ch_fasta )
 
     versions = ch_versions.mix(ALIGN.out.versions).mix(BAM_STATS.out.versions)
 

diff --git a/subworkflows/local/mapping/map_to_ref/main.nf b/subworkflows/local/mapping/map_to_ref/main.nf
@@ -13,19 +13,19 @@ workflow MAP_TO_REF {
         .join(ch_refs)
         .set { ch_map_ref_in }
 
-    ALIGN(ch_map_ref_in, true, 'bai', false, false)
+    ALIGN(ch_map_ref_in, true, 'csi', false, false)
 
     ALIGN.out.bam.set { ch_aln_to_ref_bam }
 
     ch_aln_to_ref_bam
         .join(ALIGN.out.index)
-        .set { ch_aln_to_ref_bam_bai }
+        .set { ch_aln_to_ref_bam_csi }
 
     ch_map_ref_in
         .map { meta, _reads, fasta -> [meta, fasta] }
         .set { ch_fasta }
 
-    BAM_STATS(ch_aln_to_ref_bam_bai, ch_fasta)
+    BAM_STATS(ch_aln_to_ref_bam_csi, ch_fasta)
 
     versions = ch_versions.mix(ALIGN.out.versions).mix(BAM_STATS.out.versions)
 

diff --git a/subworkflows/local/polishing/pilon/polish_pilon/main.nf b/subworkflows/local/polishing/pilon/polish_pilon/main.nf
@@ -19,7 +19,7 @@ workflow POLISH_PILON {
 
     ch_versions = ch_versions.mix(MAP_SR.out.versions)
 
-    RUN_PILON(assembly, MAP_SR.out.aln_to_assembly_bam_bai)
+    RUN_PILON(assembly, MAP_SR.out.aln_to_assembly_bam_csi)
 
     RUN_PILON.out.improved_assembly.set { pilon_polished }
 

diff --git a/subworkflows/local/polishing/pilon/run_pilon/main.nf b/subworkflows/local/polishing/pilon/run_pilon/main.nf
@@ -3,15 +3,15 @@ include { PILON } from '../../../../../modules/nf-core/pilon/main'
 workflow RUN_PILON {
     take:
     assembly_in
-    aln_to_assembly_bam_bai
+    aln_to_assembly_bam_csi
 
     main:
     assembly_in
-        .join(aln_to_assembly_bam_bai)
+        .join(aln_to_assembly_bam_csi)
         .set { pilon_in }
     PILON(
-        pilon_in.map { meta, assembly, _bam, _bai -> [meta, assembly] },
-        pilon_in.map { meta, _assembly, bam, bai -> [meta, bam, bai] },
+        pilon_in.map { meta, assembly, _bam, _csi -> [meta, assembly] },
+        pilon_in.map { meta, _assembly, bam, csi -> [meta, bam, csi] },
         "bam",
     )
     versions = PILON.out.versions

diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf