From a3496d0c744ab94f4d1551615413836fd6755e26 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Tue, 5 May 2026 22:31:28 +0200
Subject: [PATCH 1/3] removed fai from bowtie2/build

---
 modules/nf-core/bowtie2/build/main.nf            | 2 +-
 modules/nf-core/bowtie2/build/meta.yml           | 6 ------
 modules/nf-core/bowtie2/build/tests/main.nf.test | 3 +--
 3 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 84798da37804..ee4b14f983e2 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -8,7 +8,7 @@ process BOWTIE2_BUILD {
         'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }"
 
     input:
-    tuple val(meta), path(fasta), path(fai)
+    tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path('bowtie2')    , emit: index
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
index ce1b2ba7fed7..e2a4367c0afa 100644
--- a/modules/nf-core/bowtie2/build/meta.yml
+++ b/modules/nf-core/bowtie2/build/meta.yml
@@ -28,12 +28,6 @@ input:
         pattern: "*.{fa,fasta,fna}"
         ontologies:
           - edam: "http://edamontology.org/format_1929"
-    - fai:
-        type: file
-        description: Reference genome FASTA index file
-        pattern: "*.{fai}"
-        ontologies:
-          - edam: "http://edamontology.org/format_3326"
 output:
   index:
     - - meta:
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
index ba4a2f6eb6e9..a4bad2a10f75 100644
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test
@@ -15,8 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }

From 139c03470cce875e0775b8c6f36104da00e77b29 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Tue, 5 May 2026 22:36:26 +0200
Subject: [PATCH 2/3] removed fai index from bowtie2/align input

---
 modules/nf-core/bowtie2/align/main.nf         |  2 +-
 modules/nf-core/bowtie2/align/meta.yml        |  6 --
 .../nf-core/bowtie2/align/tests/main.nf.test  | 78 +++++++------------
 3 files changed, 27 insertions(+), 59 deletions(-)

diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
index 5e5eb70a7538..9be0dfeeef18 100644
--- a/modules/nf-core/bowtie2/align/main.nf
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -10,7 +10,7 @@ process BOWTIE2_ALIGN {
     input:
     tuple val(meta) , path(reads)
     tuple val(meta2), path(index)
-    tuple val(meta3), path(fasta), path(fai)
+    tuple val(meta3), path(fasta)
     val   save_unaligned
     val   sort_bam
 
diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
index 869ae3d88106..83e1487cdbb8 100644
--- a/modules/nf-core/bowtie2/align/meta.yml
+++ b/modules/nf-core/bowtie2/align/meta.yml
@@ -50,12 +50,6 @@ input:
         pattern: "*.{fa,fasta,fna}"
         ontologies:
           - edam: "http://edamontology.org/format_1929"
-    - fai:
-        type: file
-        description: Reference genome FASTA index file
-        pattern: "*.{fai}"
-        ontologies:
-          - edam: "http://edamontology.org/format_3326"
   - save_unaligned:
       type: boolean
       description: |
diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test
index 65f8c124fcc1..214c97cc105d 100644
--- a/modules/nf-core/bowtie2/align/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/align/tests/main.nf.test
@@ -18,8 +18,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -36,8 +35,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -69,8 +67,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -87,8 +84,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -120,8 +116,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -138,8 +133,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -170,8 +164,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -188,8 +181,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -220,8 +212,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -241,8 +232,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -273,8 +263,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -294,8 +283,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -327,8 +315,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -345,8 +332,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -378,8 +364,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -399,8 +384,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -431,8 +415,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -452,8 +435,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -484,8 +466,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -502,8 +483,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -536,8 +516,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -557,8 +536,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
@@ -588,8 +566,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -609,8 +586,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
@@ -643,8 +619,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -661,8 +636,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[3] = false //save_unaligned
                 input[4] = false //sort

From 0581360fed4843be66f612807740686df175d323 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Tue, 5 May 2026 23:38:17 +0200
Subject: [PATCH 3/3] updated modules and subworkflows that depend on bowtie2
 modules

---
 .../buildfromindex/tests/main.nf.test         |  6 ++---
 .../fastqscreen/tests/main.nf.test            |  6 ++---
 .../nf-core/hostile/clean/tests/main.nf.test  |  3 +--
 modules/nf-core/vamb/bin/tests/main.nf.test   | 24 +++++++------------
 subworkflows/nf-core/fasta_index_dna/main.nf  | 10 +-------
 .../nf-core/fastq_align_bowtie2/main.nf       |  6 ++++-
 .../fastq_align_bowtie2/tests/main.nf.test    | 12 ++++------
 subworkflows/nf-core/fastq_align_dna/main.nf  |  9 +------
 .../fastq_align_dna/tests/main.nf.test        |  6 ++---
 .../tests/main.nf.test                        |  6 ++---
 .../tests/main.nf.test                        |  3 +--
 .../nf-core/fastq_remove_rrna/main.nf         |  6 ++---
 12 files changed, 32 insertions(+), 65 deletions(-)

diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
index ba8e05c40cc1..d8bec478b3dd 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
+++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
@@ -18,12 +18,10 @@ nextflow_process {
                 """
                 input[0] = channel.of([
                     [id: "sarscov2"],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ], [
                     [id: "human"],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                 ])
                 """
             }
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
index 8b8e7ac79718..99012d733e79 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
@@ -21,12 +21,10 @@ nextflow_process {
                 """
                 input[0] = channel.of([
                     [id: "sarscov2"],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ], [
                     [id: "human"],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                 ])
                 """
             }
diff --git a/modules/nf-core/hostile/clean/tests/main.nf.test b/modules/nf-core/hostile/clean/tests/main.nf.test
index b75b49218ca2..0c671d23d227 100644
--- a/modules/nf-core/hostile/clean/tests/main.nf.test
+++ b/modules/nf-core/hostile/clean/tests/main.nf.test
@@ -18,8 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/vamb/bin/tests/main.nf.test b/modules/nf-core/vamb/bin/tests/main.nf.test
index 3d869675cab1..d0f626c7171d 100644
--- a/modules/nf-core/vamb/bin/tests/main.nf.test
+++ b/modules/nf-core/vamb/bin/tests/main.nf.test
@@ -27,8 +27,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     """
                 }
@@ -51,8 +50,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     input[3] = false
                     input[4] = true
@@ -140,8 +138,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     """
                 }
@@ -164,8 +161,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     input[3] = false
                     input[4] = true
@@ -230,8 +226,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     """
                 }
@@ -254,8 +249,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     input[3] = false
                     input[4] = true
@@ -348,8 +342,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     """
                 }
@@ -372,8 +365,7 @@ nextflow_process {
                         file(
                             "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/mag/assemblies/SPAdes-test_minigut_contigs.fasta.gz",
                             checkIfExists: true
-                        ),
-                        []
+                        )
                     ]
                     input[3] = false
                     input[4] = true
diff --git a/subworkflows/nf-core/fasta_index_dna/main.nf b/subworkflows/nf-core/fasta_index_dna/main.nf
index a1a0564197ed..e2e123b1454b 100644
--- a/subworkflows/nf-core/fasta_index_dna/main.nf
+++ b/subworkflows/nf-core/fasta_index_dna/main.nf
@@ -29,15 +29,7 @@ workflow FASTA_INDEX_DNA {
 
     // Handle different aligners using conditional logic
     if (val_aligner == 'bowtie2') {
-
-        /*
-        This is a temporary fix until all aligner handle ch_fasta_fai
-        */
-        ch_fasta_fai = ch_fasta.map { meta, fasta ->
-            tuple(meta, fasta, [])
-        }
-
-        BOWTIE2_BUILD(ch_fasta_fai)
+        BOWTIE2_BUILD(ch_fasta)
         ch_aligner_index = BOWTIE2_BUILD.out.index
     } else if (val_aligner == 'bwamem') {
         BWAMEM1_INDEX(ch_fasta)
diff --git a/subworkflows/nf-core/fastq_align_bowtie2/main.nf b/subworkflows/nf-core/fastq_align_bowtie2/main.nf
index 67df44ef687a..8c1a19f5e414 100644
--- a/subworkflows/nf-core/fastq_align_bowtie2/main.nf
+++ b/subworkflows/nf-core/fastq_align_bowtie2/main.nf
@@ -15,10 +15,14 @@ workflow FASTQ_ALIGN_BOWTIE2 {
 
     main:
 
+    //
+    // Remap ch_fasta_fai to ch_fasta
+    ch_fasta = ch_fasta_fai.map{ meta, fasta, _fai -> [ meta, fasta] }
+
     //
     // Map reads with Bowtie2
     //
-    BOWTIE2_ALIGN(ch_reads, ch_index, ch_fasta_fai, save_unaligned, sort_bam)
+    BOWTIE2_ALIGN(ch_reads, ch_index, ch_fasta, save_unaligned, sort_bam)
 
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
diff --git a/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test
index d8ad00bf0c07..975a239914f6 100644
--- a/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test
@@ -21,8 +21,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
@@ -70,8 +69,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
@@ -126,8 +124,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
@@ -178,8 +175,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
diff --git a/subworkflows/nf-core/fastq_align_dna/main.nf b/subworkflows/nf-core/fastq_align_dna/main.nf
index 410d02584d92..920d7641ade2 100644
--- a/subworkflows/nf-core/fastq_align_dna/main.nf
+++ b/subworkflows/nf-core/fastq_align_dna/main.nf
@@ -31,14 +31,7 @@ workflow FASTQ_ALIGN_DNA {
     // Align fastq files to reference genome and (optionally) sort
     if (aligner == 'bowtie2') {
 
-        /*
-        This is a temporary fix until all aligner handle ch_fasta_fai
-        */
-        ch_fasta_fai = ch_fasta.map { meta, fasta ->
-            tuple(meta, fasta, [])
-        }
-
-        BOWTIE2_ALIGN(ch_reads, ch_aligner_index, ch_fasta_fai, false, sort)
+        BOWTIE2_ALIGN(ch_reads, ch_aligner_index, ch_fasta, false, sort)
         // if aligner is bowtie2
         ch_bam = ch_bam.mix(BOWTIE2_ALIGN.out.bam)
     }
diff --git a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test
index 1e914c3d0725..793245eabd32 100644
--- a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test
@@ -32,8 +32,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
@@ -72,8 +71,7 @@ nextflow_workflow {
                     """
                     input[0] = Channel.value([
                         [ id:'genome' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ])
                     """
                 }
diff --git a/subworkflows/nf-core/fastq_decontaminate_deacon_hostile/tests/main.nf.test b/subworkflows/nf-core/fastq_decontaminate_deacon_hostile/tests/main.nf.test
index d724cb532604..397cb18972e2 100644
--- a/subworkflows/nf-core/fastq_decontaminate_deacon_hostile/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_decontaminate_deacon_hostile/tests/main.nf.test
@@ -26,8 +26,7 @@ nextflow_workflow {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -67,8 +66,7 @@ nextflow_workflow {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
diff --git a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test
index 19b015f1634c..10fc6a50a660 100644
--- a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test
@@ -20,8 +20,7 @@ nextflow_workflow {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/subworkflows/nf-core/fastq_remove_rrna/main.nf b/subworkflows/nf-core/fastq_remove_rrna/main.nf
index 112ef62ed18d..c0dcc5a5f926 100644
--- a/subworkflows/nf-core/fastq_remove_rrna/main.nf
+++ b/subworkflows/nf-core/fastq_remove_rrna/main.nf
@@ -138,7 +138,7 @@ workflow FASTQ_REMOVE_RRNA {
             SEQKIT_REPLACE_U2T.out.fastx
                 .map { _meta, fasta_file -> fasta_file }
                 .collectFile(name: 'rrna_combined_dna.fasta', newLine: true)
-                .map { fasta_file -> [[id: 'rrna_refs'], fasta_file, []] }
+                .map { fasta_file -> [[id: 'rrna_refs'], fasta_file] }
                 .set { ch_combined_fasta }
 
             BOWTIE2_BUILD(
@@ -161,7 +161,7 @@ workflow FASTQ_REMOVE_RRNA {
         BOWTIE2_ALIGN(
             ch_reads_for_bowtie2.single_end,
             ch_bowtie2_index,
-            [[], [], []],  // No reference fasta needed
+            [[], []],  // No reference fasta needed
             true,      // save_unaligned - for single-end this works correctly
             false,     // sort_bam - not needed
         )
@@ -175,7 +175,7 @@ workflow FASTQ_REMOVE_RRNA {
         BOWTIE2_ALIGN_PE(
             ch_reads_for_bowtie2.paired_end,
             ch_bowtie2_index,
-            [[], [], []],  // No reference fasta needed for BAM output
+            [[], []],  // No reference fasta needed for BAM output
             false,     // save_unaligned - we'll extract from BAM instead
             false,     // sort_bam - not needed
         )