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Update Rundbcan modules #9768

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04a74a1
update rundbcan modules
HaidYi Jan 25, 2026
cd0f972
make dbCAN substrate output optional
HaidYi Jan 26, 2026
47f6f86
make dbCAN easyCGC and easySubstrate work as well
HaidYi Jan 26, 2026
134ea35
make output optional
HaidYi Jan 26, 2026
9ace581
update snapshot
HaidYi Jan 26, 2026
f4590a1
update to 5.2.5
HaidYi Jan 28, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/rundbcan/cazymeannotation/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- bioconda
- conda-forge
dependencies:
- bioconda::dbcan=5.1.2
- bioconda::dbcan=5.2.4
10 changes: 6 additions & 4 deletions modules/nf-core/rundbcan/cazymeannotation/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process RUNDBCAN_CAZYMEANNOTATION {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dbcan:5.1.2--pyhdfd78af_0' :
'biocontainers/dbcan:5.1.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' :
'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }"

input:
tuple val(meta), path(input_raw_data)
Expand All @@ -14,7 +14,7 @@ process RUNDBCAN_CAZYMEANNOTATION {
output:
tuple val(meta), path("${prefix}_overview.tsv") , emit: cazyme_annotation
tuple val(meta), path("${prefix}_dbCAN_hmm_results.tsv") , emit: dbcanhmm_results
tuple val(meta), path("${prefix}_dbCANsub_hmm_results.tsv"), emit: dbcansub_results
tuple val(meta), path("${prefix}_dbCANsub_hmm_results.tsv"), emit: dbcansub_results, optional: true
tuple val(meta), path("${prefix}_diamond.out") , emit: dbcandiamond_results
path "versions.yml" , emit: versions

Expand All @@ -34,7 +34,9 @@ process RUNDBCAN_CAZYMEANNOTATION {

mv overview.tsv ${prefix}_overview.tsv
mv dbCAN_hmm_results.tsv ${prefix}_dbCAN_hmm_results.tsv
mv dbCANsub_hmm_results.tsv ${prefix}_dbCANsub_hmm_results.tsv
if [ -f dbCANsub_hmm_results.tsv ]; then
mv dbCANsub_hmm_results.tsv ${prefix}_dbCANsub_hmm_results.tsv
fi
mv diamond.out ${prefix}_diamond.out

cat <<-END_VERSIONS > versions.yml
Expand Down
40 changes: 15 additions & 25 deletions modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
]
],
"4": [
"versions.yml:md5,40f0cf24dce2629d444781eaee026c7f"
"versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2"
],
"cazyme_annotation": [
[
Expand Down Expand Up @@ -70,20 +70,20 @@
]
],
"versions": [
"versions.yml:md5,40f0cf24dce2629d444781eaee026c7f"
"versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2"
]
},
{
"RUNDBCAN_CAZYMEANNOTATION": {
"dbcan": "5.1.2"
"dbcan": "5.2.4"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-06-12T17:00:00.485809769"
"timestamp": "2026-01-16T11:22:59.260712"
},
"dbcancazyme - simplified": {
"content": [
Expand All @@ -93,7 +93,7 @@
{
"id": "test"
},
"test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54"
"test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d"
]
],
"1": [
Expand All @@ -105,38 +105,33 @@
]
],
"2": [
[
{
"id": "test"
},
"test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b"
]
Comment on lines -108 to -113
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@mashehu mashehu Jan 26, 2026

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is this empty output expected with the version update?

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@HaidYi HaidYi Jan 26, 2026

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Yes, the software updates output logic a bit. @Xinpeng021001 Could you explain the reason here?

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@Xinpeng021001 Xinpeng021001 Jan 26, 2026

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@mashehu hi, based on the test data we have on nf-core, we cannot generate the expected results, and that's why we create the empty output. We use HMMdbs for the run_dbcan which is strict to get results.

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@Xinpeng021001 Xinpeng021001 Jan 26, 2026

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I'm working on a new version and once it is merged I'll add it as the newest version here.


],
"3": [
[
{
"id": "test"
},
"test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84"
"test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e"
]
],
"4": [
"versions.yml:md5,40f0cf24dce2629d444781eaee026c7f"
"versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2"
],
"cazyme_annotation": [
[
{
"id": "test"
},
"test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54"
"test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d"
]
],
"dbcandiamond_results": [
[
{
"id": "test"
},
"test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84"
"test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e"
]
],
"dbcanhmm_results": [
Expand All @@ -148,27 +143,22 @@
]
],
"dbcansub_results": [
[
{
"id": "test"
},
"test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b"
]

],
"versions": [
"versions.yml:md5,40f0cf24dce2629d444781eaee026c7f"
"versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2"
]
},
{
"RUNDBCAN_CAZYMEANNOTATION": {
"dbcan": "5.1.2"
"dbcan": "5.2.4"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
"nextflow": "25.04.6"
},
"timestamp": "2025-06-12T16:59:56.40131421"
"timestamp": "2026-01-25T22:59:36.085431385"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/rundbcan/database/environment.yml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- bioconda
- conda-forge
dependencies:
- bioconda::dbcan=5.1.2
- bioconda::dbcan=5.2.4
7 changes: 4 additions & 3 deletions modules/nf-core/rundbcan/database/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process RUNDBCAN_DATABASE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dbcan:5.1.2--pyhdfd78af_0' :
'biocontainers/dbcan:5.1.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' :
'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }"

output:
path "dbcan_db" , emit: dbcan_db
Expand All @@ -17,7 +17,8 @@ process RUNDBCAN_DATABASE {
def args = task.ext.args ?: ''
"""
run_dbcan database \\
--db_dir dbcan_db
--db_dir dbcan_db \\
--aws_s3

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/rundbcan/database/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,36 +2,36 @@
"rundbcan - database - basic": {
"content": [
[
"versions.yml:md5,b064fe90159963e182ec980f0f4677c5"
"versions.yml:md5,38287a7d6ca60d8c01ccbd6bb4def88e"
],
{
"RUNDBCAN_DATABASE": {
"dbcan": "5.1.2"
"dbcan": "5.2.4"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-06-12T17:01:26.958626278"
"timestamp": "2026-01-16T13:09:03.917376"
},
"rundbcan - database - stub": {
"content": [
"dbcan_db",
[
"versions.yml:md5,b064fe90159963e182ec980f0f4677c5"
"versions.yml:md5,38287a7d6ca60d8c01ccbd6bb4def88e"
],
{
"RUNDBCAN_DATABASE": {
"dbcan": "5.1.2"
"dbcan": "5.2.4"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-06-12T17:01:31.197377024"
"timestamp": "2026-01-16T13:09:07.918572"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/rundbcan/easycgc/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- bioconda
- conda-forge
dependencies:
- bioconda::dbcan=5.1.2
- bioconda::dbcan=5.2.4
16 changes: 10 additions & 6 deletions modules/nf-core/rundbcan/easycgc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process RUNDBCAN_EASYCGC {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dbcan:5.1.2--pyhdfd78af_0' :
'biocontainers/dbcan:5.1.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' :
'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }"

input:
tuple val(meta), path(input_raw_data)
Expand All @@ -15,12 +15,12 @@ process RUNDBCAN_EASYCGC {
output:
tuple val(meta), path("${prefix}_overview.tsv") , emit: cazyme_annotation
tuple val(meta), path("${prefix}_dbCAN_hmm_results.tsv") , emit: dbcanhmm_results
tuple val(meta), path("${prefix}_dbCANsub_hmm_results.tsv"), emit: dbcansub_results
tuple val(meta), path("${prefix}_dbCANsub_hmm_results.tsv"), emit: dbcansub_results, optional: true
tuple val(meta), path("${prefix}_diamond.out") , emit: dbcandiamond_results
tuple val(meta), path("${prefix}_cgc.gff") , emit: cgc_gff
tuple val(meta), path("${prefix}_cgc_standard_out.tsv") , emit: cgc_standard_out
tuple val(meta), path("${prefix}_diamond.out.tc") , emit: diamond_out_tc
tuple val(meta), path("${prefix}_TF_hmm_results.tsv") , emit: tf_hmm_results
tuple val(meta), path("${prefix}_TF_hmm_results.tsv") , emit: tf_hmm_results, optional: true
tuple val(meta), path("${prefix}_STP_hmm_results.tsv") , emit: stp_hmm_results
path "versions.yml" , emit: versions

Expand All @@ -42,14 +42,18 @@ process RUNDBCAN_EASYCGC {

mv overview.tsv ${prefix}_overview.tsv
mv dbCAN_hmm_results.tsv ${prefix}_dbCAN_hmm_results.tsv
mv dbCANsub_hmm_results.tsv ${prefix}_dbCANsub_hmm_results.tsv
if [ -f dbCANsub_hmm_results.tsv ]; then
mv dbCANsub_hmm_results.tsv ${prefix}_dbCANsub_hmm_results.tsv
fi
mv diamond.out ${prefix}_diamond.out
mv cgc.gff ${prefix}_cgc.gff
mv cgc_standard_out.tsv ${prefix}_cgc_standard_out.tsv
mv diamond.out.tc ${prefix}_diamond.out.tc
mv TF_hmm_results.tsv ${prefix}_TF_hmm_results.tsv
mv STP_hmm_results.tsv ${prefix}_STP_hmm_results.tsv
mv total_cgc_info.tsv ${prefix}_total_cgc_info.tsv
if [ -f TF_hmm_results.tsv ]; then
mv TF_hmm_results.tsv ${prefix}_TF_hmm_results.tsv
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
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