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Merged
dialvarezs merged 18 commits into from
Apr 6, 2026
Merged

feat(coverm/{contig,genome}): add bam output #11111

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959c98d
feat: add bam output to coverm/contig
dialvarezs Apr 1, 2026
751c5e9
chore: quotes
dialvarezs Apr 1, 2026
3ac57f6
chore: update meta
dialvarezs Apr 1, 2026
df75c2c
Merge branch 'master' into update-coverm
dialvarezs Apr 1, 2026
bc9c71b
chore: fix meta
dialvarezs Apr 1, 2026
48b24d5
Merge branch 'update-coverm' of github.com:dialvarezs/nf-core-modules…
dialvarezs Apr 1, 2026
28f9fcd
chore: format meta
dialvarezs Apr 1, 2026
070a01b
feat: add bam output to coverm/genome
dialvarezs Apr 1, 2026
aee6710
chore: meta fmt
dialvarezs Apr 1, 2026
abfac8a
chore: meta input fix
dialvarezs Apr 1, 2026
303e363
fix: meta input order
dialvarezs Apr 1, 2026
34144bf
fix: include bam filenames only for stability
dialvarezs Apr 1, 2026
93aea6c
chore: re-freeze container
dialvarezs Apr 1, 2026
f0784b9
chore: reorder inputs, add ontologies
dialvarezs Apr 2, 2026
199961c
fix: snapshot parameters
dialvarezs Apr 2, 2026
f2280c4
feat: improve snapshots and unify naming
dialvarezs Apr 2, 2026
44b6b2c
feat: add reads checksum from bam
dialvarezs Apr 2, 2026
d9d71aa
Merge branch 'master' into update-coverm
prototaxites Apr 2, 2026
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32 changes: 20 additions & 12 deletions modules/nf-core/coverm/contig/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,43 +3,51 @@ process COVERM_CONTIG {
label "process_medium"

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/coverm:0.7.0--hcb7b614_4' :
'biocontainers/coverm:0.7.0--hcb7b614_4' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c4402aed2ff8bd062a013369c9049e68bdd159e849b271a227a8ce2727e941e1/data'
: 'community.wave.seqera.io/library/coverm:0.7.0--c57cbb9db4d660fb'}"

input:
tuple val(meta), path(input)
tuple val(meta2), path(reference)
val bam_input
val interleaved
val enable_bam_output
Comment on lines 11 to +15
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@famosab famosab Apr 2, 2026

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Can we put all these inputs into one tuple? That will make sure you're sure that EVERY time everything comes together in the right combination.

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@dialvarezs dialvarezs Apr 2, 2026 •
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You mean this?

tuple val(meta), path(input), path(reference), val(bam_input), val(interleaved), val(enable_bam_output)

I'm not so sure about that. In my opinion that would introduce extra complexity in the workflows, because you will have to build the channel by joining/combinig all together.
And other similar modules use this pattern too: minimap2, bwa, bowtie. All of them separates the reads, the reference and additional flags as separate inputs.

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@famosab famosab Apr 2, 2026

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I get that, we just try to converge more on that because the combine statements make sure that the channels do not get mixed up, but its more of a goal and not something I would enforce here.

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@prototaxites prototaxites Apr 2, 2026

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I don't think it's a bad idea to put most of these as a single input, as they're sample-dependent vals - but presumably enable_bam_output is something you'd want to configure once as a single input?


output:
tuple val(meta), path("*.depth.txt"), emit: coverage
tuple val(meta), path('*.depth.tsv'), emit: coverage
tuple val(meta), path('*.bam') , emit: bam, optional: true
tuple val("${task.process}"), val('coverm'), eval('coverm --version | sed "s/coverm //"'), emit: versions_coverm, topic: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def fastq_input = meta.single_end ? "--single" : interleaved ? "--interleaved" : "--coupled"
def input_type = bam_input ? "--bam-files" : "${fastq_input}"
def reference_str = bam_input ? "" : "--reference ${reference}"
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def fastq_input = meta.single_end ? "--single" : interleaved ? "--interleaved" : "--coupled"
def input_type = bam_input ? "--bam-files" : "${fastq_input}"

def reference_str = bam_input ? "" : "--reference ${reference}"
def bam_output_str = enable_bam_output ? "--bam-file-cache-directory _bam_cache/" : ""
"""
TMPDIR=.

coverm contig \\
--threads ${task.cpus} \\
${input_type} ${input} \\
${reference_str} \\
${bam_output_str} \\
${args} \\
--output-file ${prefix}.depth.txt
--output-file ${prefix}.depth.tsv

mv _bam_cache/*.bam . || true
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
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"""
touch ${prefix}.depth.txt
touch ${prefix}.depth.tsv
touch ${prefix}.bam
"""
}
36 changes: 28 additions & 8 deletions modules/nf-core/coverm/contig/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`

- input:
type: file
description: |
Expand All @@ -32,6 +31,8 @@ input:
pattern: "*.{fa,fq,fa.gz,fq.gz,bam}"
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
- edam: http://edamontology.org/format_2572 # BAM

- - meta2:
type: map
description: |
Expand All @@ -40,11 +41,13 @@ input:

- reference:
type: file
description: Reference FASTA file to map reads to, or minimap2/strobealign index.
description: |
Reference FASTA file to map reads to, or minimap2/strobealign index.
Not required if using BAM input.
pattern: "*.{fasta,fasta.gz,mmi,sti}"
ontologies:
- edam: http://edamontology.org/format_1929 # FASTA

ontologies: []
- bam_input:
type: boolean
description: True if input is bam files
Expand All @@ -53,20 +56,37 @@ input:
type: boolean
description: True if input is interleaved fastq file

- enable_bam_output:
type: boolean
description: True to enable BAM output of aligned reads

output:
coverage:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
pattern: "*.depths.{txt}"
- "*.depth.txt":
e.g. `[ id:'sample1' ]`
- "*.depth.tsv":
type: file
description: Tab-delimited file containing coverage information for each contig and sample.
pattern: "*.depth.tsv"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV

bam:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
pattern: "*.depths.{txt}"
e.g. `[ id:'sample1' ]`
- "*.bam":
type: file
description: BAM file containing aligned reads.
pattern: "*.bam"
ontologies:
- edam: http://edamontology.org/format_2572 # BAM

versions_coverm:
- - ${task.process}:
type: string
Expand Down
39 changes: 31 additions & 8 deletions modules/nf-core/coverm/contig/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true),
Expand All @@ -29,14 +29,24 @@ nextflow_process {
]
input[2] = false
input[3] = false
input[4] = true
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out.coverage,
process.out.bam.collect { meta, bam_files ->
[
meta,
bam_files.collect { file -> bam(file).getReadsMD5() }
]
},
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}

Expand All @@ -48,24 +58,36 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam', checkIfExists: true)
[ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam', checkIfExists: true)
]
]
input[1] = [
[],
[]
]
input[2] = true
input[3] = false
input[4] = false
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out.coverage,
process.out.bam.collect { meta, bam_files ->
[
meta,
bam_files.collect { file -> bam(file).getReadsMD5() }
]
},
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}

Expand All @@ -79,7 +101,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true),
Expand All @@ -91,14 +113,15 @@ nextflow_process {
]
input[2] = false
input[3] = false
input[4] = false
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
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