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Remove fai index from bowtie2 modules #11537

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a3496d0
removed fai from bowtie2/build
Kevin-Brockers May 5, 2026
139c034
removed fai index from bowtie2/align input
Kevin-Brockers May 5, 2026
0581360
updated modules and subworkflows that depend on bowtie2 modules
Kevin-Brockers May 5, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/bowtie2/align/main.nf
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Expand Up @@ -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

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6 changes: 0 additions & 6 deletions modules/nf-core/bowtie2/align/meta.yml
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Expand Up @@ -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: |
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78 changes: 26 additions & 52 deletions modules/nf-core/bowtie2/align/tests/main.nf.test
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2 changes: 1 addition & 1 deletion modules/nf-core/bowtie2/build/main.nf
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Expand Up @@ -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
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6 changes: 0 additions & 6 deletions modules/nf-core/bowtie2/build/meta.yml
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Expand Up @@ -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:
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3 changes: 1 addition & 2 deletions modules/nf-core/bowtie2/build/tests/main.nf.test
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Expand Up @@ -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)
]
"""
}
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6 changes: 2 additions & 4 deletions modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
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Expand Up @@ -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)
])
"""
}
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6 changes: 2 additions & 4 deletions modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
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Expand Up @@ -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)
])
"""
}
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3 changes: 1 addition & 2 deletions modules/nf-core/hostile/clean/tests/main.nf.test
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Expand Up @@ -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)
]
"""
}
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24 changes: 8 additions & 16 deletions modules/nf-core/vamb/bin/tests/main.nf.test
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Expand Up @@ -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
),
[]
)
]
"""
}
Expand All @@ -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
Expand Down Expand Up @@ -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
),
[]
)
]
"""
}
Expand All @@ -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
Expand Down Expand Up @@ -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
),
[]
)
]
"""
}
Expand All @@ -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
Expand Down Expand Up @@ -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
),
[]
)
]
"""
}
Expand All @@ -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
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10 changes: 1 addition & 9 deletions subworkflows/nf-core/fasta_index_dna/main.nf
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Expand Up @@ -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)
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6 changes: 5 additions & 1 deletion subworkflows/nf-core/fastq_align_bowtie2/main.nf
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Expand Up @@ -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
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12 changes: 4 additions & 8 deletions subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test
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Expand Up @@ -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)
])
"""
}
Expand Down Expand Up @@ -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)
])
"""
}
Expand Down Expand Up @@ -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)
])
"""
}
Expand Down Expand Up @@ -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)
])
"""
}
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9 changes: 1 addition & 8 deletions subworkflows/nf-core/fastq_align_dna/main.nf
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Expand Up @@ -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)
}
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6 changes: 2 additions & 4 deletions subworkflows/nf-core/fastq_align_dna/tests/main.nf.test
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Expand Up @@ -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)
])
"""
}
Expand Down Expand Up @@ -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)
])
"""
}
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6 changes: 2 additions & 4 deletions subworkflows/nf-core/fastq_decontaminate_deacon_hostile/tests/main.nf.test
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Expand Up @@ -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)
]
"""
}
Expand Down Expand Up @@ -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)
]
"""
}
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3 changes: 1 addition & 2 deletions subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test
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Expand Up @@ -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)
]
"""
}
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6 changes: 3 additions & 3 deletions subworkflows/nf-core/fastq_remove_rrna/main.nf
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Expand Up @@ -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(
Expand All @@ -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
)
Expand All @@ -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
)
Expand Down
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