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feat: allow bwa-mem to output sam format #11457

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fca7ba4
feat: allow bwa-mem to output sam format
piplus2 May 1, 2026
5d3695b
chore: updated snapshots
piplus2 May 1, 2026
e057016
update: meta.yml includes sam output
piplus2 May 1, 2026
35542fb
update: added process.out.sam to match the process
piplus2 May 7, 2026
b90e4cd
updated snapshots to match the new test
piplus2 May 7, 2026
7a7da45
added 2 tests for sam output
piplus2 May 7, 2026
b84f186
fix end of file
piplus2 May 7, 2026
e04edc0
fix: adhere to test specifications
piplus2 May 7, 2026
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12 changes: 11 additions & 1 deletion modules/nf-core/bwa/mem/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ process BWA_MEM {
output:
tuple val(meta), path("*.bam") , emit: bam, optional: true
tuple val(meta), path("*.cram") , emit: cram, optional: true
tuple val(meta), path("*.sam") , emit: sam, optional: true
tuple val(meta), path("*.csi") , emit: csi, optional: true
tuple val(meta), path("*.crai") , emit: crai, optional: true
tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa
Expand All @@ -36,6 +37,15 @@ process BWA_MEM {
"bam"
def reference = fasta && extension=="cram" ? "--reference ${fasta}" : ""
if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
//
// For SAM output we can skip samtools view
//
def pipe_command = ""
if (extension == "sam") {
pipe_command = "> ${prefix}.${extension}"
} else {
pipe_command = "| samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -"
}
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`

Expand All @@ -44,7 +54,7 @@ process BWA_MEM {
-t $task.cpus \\
\$INDEX \\
$reads \\
| samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -
$pipe_command
"""

stub:
Expand Down
10 changes: 10 additions & 0 deletions modules/nf-core/bwa/mem/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,16 @@ output:
pattern: "*.{cram}"
ontologies:
- edam: "http://edamontology.org/format_3462"
sam:
- - meta:
type: map
description: Groovy Map containing sample information
- "*.sam":
type: file
description: Output SAM file containing read alignments
pattern: "*.{sam}"
ontologies:
- edam: "http://edamontology.org/format_2573"
csi:
- - meta:
type: map
Expand Down
88 changes: 88 additions & 0 deletions modules/nf-core/bwa/mem/tests/main.nf.test
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@famosab famosab May 7, 2026

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Can you add a test where you actually expect the sam file in the output please? :)

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@piplus2 piplus2 May 7, 2026

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I've just added process.out.sam, do you think it may be worth writing a specific test for the sam only? I did not include it to match the cram, csi and crai.

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@famosab famosab May 7, 2026

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in theory we should test each output properly. So yes please add it :) The way its done for nw we can already see that sam is not created when it should not be created (which is good).

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@piplus2 piplus2 May 7, 2026

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Yes, I'll do it :)

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@piplus2 piplus2 May 7, 2026

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I've added 2 tests (single and paired read) to check that we actually get a sam output.

Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.cram,
process.out.sam,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
Expand Down Expand Up @@ -80,6 +81,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.cram,
process.out.sam,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
Expand All @@ -91,6 +93,47 @@ nextflow_process {

}

test("Single-End - SAM output") {

config "./nextflow_sam.config"

when {
params {
module_args = "--output-fmt sam"
}

process {
"""
input[0] = [
[ id:'test', single_end:true ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
]
input[1] = BWA_INDEX.out.index
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.cram,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
bam(process.out.sam[0][1]).getReadsMD5()
).match()
}
)
}

}

test("Paired-End") {

when {
Expand All @@ -115,6 +158,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.cram,
process.out.sam,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
Expand Down Expand Up @@ -150,6 +194,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.cram,
process.out.sam,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
Expand Down Expand Up @@ -185,6 +230,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.cram,
process.out.sam,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
Expand All @@ -196,6 +242,48 @@ nextflow_process {

}

test ("Paired-end - SAM output") {

config "./nextflow_sam.config"

when {
params {
module_args = "--output-fmt sam"
}

process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]
input[1] = BWA_INDEX.out.index
input[2] = [[:],[]]
input[3] = false
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.cram,
process.out.csi,
process.out.crai,
process.out.findAll { key, val -> key.startsWith("versions") },
bam(process.out.sam[0][1]).getReadsMD5()
).match()
}
)
}

}

test("Single-end - stub") {

options "-stub"
Expand Down
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