From 04a74a18131cce3203dd3a3f6c7e44066aec2bca Mon Sep 17 00:00:00 2001 From: HaidYi Date: Sun, 25 Jan 2026 16:14:21 -0600 Subject: [PATCH 1/6] update rundbcan modules --- .../rundbcan/cazymeannotation/environment.yml | 2 +- modules/nf-core/rundbcan/cazymeannotation/main.nf | 4 ++-- .../cazymeannotation/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/rundbcan/database/environment.yml | 2 +- modules/nf-core/rundbcan/database/main.nf | 7 ++++--- .../rundbcan/database/tests/main.nf.test.snap | 12 ++++++------ modules/nf-core/rundbcan/easycgc/environment.yml | 2 +- modules/nf-core/rundbcan/easycgc/main.nf | 4 ++-- .../nf-core/rundbcan/easysubstrate/environment.yml | 2 +- modules/nf-core/rundbcan/easysubstrate/main.nf | 4 ++-- 10 files changed, 24 insertions(+), 23 deletions(-) diff --git a/modules/nf-core/rundbcan/cazymeannotation/environment.yml b/modules/nf-core/rundbcan/cazymeannotation/environment.yml index 6d9a56aef7fe..cd7f801ab90d 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/environment.yml +++ b/modules/nf-core/rundbcan/cazymeannotation/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::dbcan=5.1.2 + - bioconda::dbcan=5.2.4 diff --git a/modules/nf-core/rundbcan/cazymeannotation/main.nf b/modules/nf-core/rundbcan/cazymeannotation/main.nf index 208bd4bd57d8..d6b378d11544 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/main.nf +++ b/modules/nf-core/rundbcan/cazymeannotation/main.nf @@ -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:5.2.4--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data) diff --git a/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap b/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap index cf210a60fa0e..35dc98e4724d 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap +++ b/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap @@ -35,7 +35,7 @@ ] ], "4": [ - "versions.yml:md5,40f0cf24dce2629d444781eaee026c7f" + "versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2" ], "cazyme_annotation": [ [ @@ -70,12 +70,12 @@ ] ], "versions": [ - "versions.yml:md5,40f0cf24dce2629d444781eaee026c7f" + "versions.yml:md5,cff4b3da5009bc8bccce6f0e28bf98a2" ] }, { "RUNDBCAN_CAZYMEANNOTATION": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], @@ -83,7 +83,7 @@ "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": [ diff --git a/modules/nf-core/rundbcan/database/environment.yml b/modules/nf-core/rundbcan/database/environment.yml index 6d9a56aef7fe..cd7f801ab90d 100644 --- a/modules/nf-core/rundbcan/database/environment.yml +++ b/modules/nf-core/rundbcan/database/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::dbcan=5.1.2 + - bioconda::dbcan=5.2.4 diff --git a/modules/nf-core/rundbcan/database/main.nf b/modules/nf-core/rundbcan/database/main.nf index 617ab882859a..7b784613eff3 100644 --- a/modules/nf-core/rundbcan/database/main.nf +++ b/modules/nf-core/rundbcan/database/main.nf @@ -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:5.2.4--pyhdfd78af_0' }" output: path "dbcan_db" , emit: dbcan_db @@ -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 "${task.process}": diff --git a/modules/nf-core/rundbcan/database/tests/main.nf.test.snap b/modules/nf-core/rundbcan/database/tests/main.nf.test.snap index e54b59a8e308..e5d773e934b6 100644 --- a/modules/nf-core/rundbcan/database/tests/main.nf.test.snap +++ b/modules/nf-core/rundbcan/database/tests/main.nf.test.snap @@ -2,11 +2,11 @@ "rundbcan - database - basic": { "content": [ [ - "versions.yml:md5,b064fe90159963e182ec980f0f4677c5" + "versions.yml:md5,38287a7d6ca60d8c01ccbd6bb4def88e" ], { "RUNDBCAN_DATABASE": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], @@ -14,17 +14,17 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-06-12T17:01:26.958626278" + "timestamp": "2026-01-16T13:09:03.917376" }, "rundbcan - database - stub": { "content": [ "dbcan_db", [ - "versions.yml:md5,b064fe90159963e182ec980f0f4677c5" + "versions.yml:md5,38287a7d6ca60d8c01ccbd6bb4def88e" ], { "RUNDBCAN_DATABASE": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], @@ -32,6 +32,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-06-12T17:01:31.197377024" + "timestamp": "2026-01-16T13:09:07.918572" } } \ No newline at end of file diff --git a/modules/nf-core/rundbcan/easycgc/environment.yml b/modules/nf-core/rundbcan/easycgc/environment.yml index 6d9a56aef7fe..cd7f801ab90d 100644 --- a/modules/nf-core/rundbcan/easycgc/environment.yml +++ b/modules/nf-core/rundbcan/easycgc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::dbcan=5.1.2 + - bioconda::dbcan=5.2.4 diff --git a/modules/nf-core/rundbcan/easycgc/main.nf b/modules/nf-core/rundbcan/easycgc/main.nf index 0095e81d85b3..c61dc1d6429c 100644 --- a/modules/nf-core/rundbcan/easycgc/main.nf +++ b/modules/nf-core/rundbcan/easycgc/main.nf @@ -4,8 +4,8 @@ process RUNDBCAN_EASYCGC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dbcan:5.1.2--pyhdfd78af_0' : - 'biocontainers/dbcan:5.1.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : + 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data) diff --git a/modules/nf-core/rundbcan/easysubstrate/environment.yml b/modules/nf-core/rundbcan/easysubstrate/environment.yml index 6d9a56aef7fe..cd7f801ab90d 100644 --- a/modules/nf-core/rundbcan/easysubstrate/environment.yml +++ b/modules/nf-core/rundbcan/easysubstrate/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::dbcan=5.1.2 + - bioconda::dbcan=5.2.4 diff --git a/modules/nf-core/rundbcan/easysubstrate/main.nf b/modules/nf-core/rundbcan/easysubstrate/main.nf index 442debfcab63..4975c9900870 100644 --- a/modules/nf-core/rundbcan/easysubstrate/main.nf +++ b/modules/nf-core/rundbcan/easysubstrate/main.nf @@ -4,8 +4,8 @@ process RUNDBCAN_EASYSUBSTRATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dbcan:5.1.2--pyhdfd78af_0' : - 'biocontainers/dbcan:5.1.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : + 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data) From cd0f9729e08b98eea3a287cb52eb41c72601d21c Mon Sep 17 00:00:00 2001 From: HaidYi Date: Sun, 25 Jan 2026 20:28:26 -0600 Subject: [PATCH 2/6] make dbCAN substrate output optional --- modules/nf-core/rundbcan/cazymeannotation/main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/rundbcan/cazymeannotation/main.nf b/modules/nf-core/rundbcan/cazymeannotation/main.nf index d6b378d11544..ba70f6e171de 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/main.nf +++ b/modules/nf-core/rundbcan/cazymeannotation/main.nf @@ -14,7 +14,7 @@ process RUNDBCAN_CAZYMEANNOTATION { output: tuple val(meta), path("${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 @@ -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 ${prefix}_diamond.out cat <<-END_VERSIONS > versions.yml From 47f6f86dcd8168d3d3be5a7e4c089f954a9c8096 Mon Sep 17 00:00:00 2001 From: HaidYi Date: Sun, 25 Jan 2026 21:04:46 -0600 Subject: [PATCH 3/6] make dbCAN easyCGC and easySubstrate work as well --- modules/nf-core/rundbcan/easycgc/main.nf | 6 ++++-- modules/nf-core/rundbcan/easysubstrate/main.nf | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/rundbcan/easycgc/main.nf b/modules/nf-core/rundbcan/easycgc/main.nf index c61dc1d6429c..bee3390bf50a 100644 --- a/modules/nf-core/rundbcan/easycgc/main.nf +++ b/modules/nf-core/rundbcan/easycgc/main.nf @@ -15,7 +15,7 @@ process RUNDBCAN_EASYCGC { output: tuple val(meta), path("${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 @@ -42,7 +42,9 @@ 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 ${prefix}_cgc_standard_out.tsv diff --git a/modules/nf-core/rundbcan/easysubstrate/main.nf b/modules/nf-core/rundbcan/easysubstrate/main.nf index 4975c9900870..812aba3e58ef 100644 --- a/modules/nf-core/rundbcan/easysubstrate/main.nf +++ b/modules/nf-core/rundbcan/easysubstrate/main.nf @@ -15,7 +15,7 @@ process RUNDBCAN_EASYSUBSTRATE { output: tuple val(meta), path("${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 @@ -46,7 +46,9 @@ process RUNDBCAN_EASYSUBSTRATE { 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 ${prefix}_cgc_standard_out.tsv From 134ea357ded8495fe0274207fdc70c29a65cbd7a Mon Sep 17 00:00:00 2001 From: HaidYi Date: Sun, 25 Jan 2026 22:31:08 -0600 Subject: [PATCH 4/6] make output optional --- modules/nf-core/rundbcan/easycgc/main.nf | 6 ++++-- modules/nf-core/rundbcan/easysubstrate/main.nf | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/rundbcan/easycgc/main.nf b/modules/nf-core/rundbcan/easycgc/main.nf index bee3390bf50a..827d026b9395 100644 --- a/modules/nf-core/rundbcan/easycgc/main.nf +++ b/modules/nf-core/rundbcan/easycgc/main.nf @@ -20,7 +20,7 @@ process RUNDBCAN_EASYCGC { tuple val(meta), path("${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 @@ -49,9 +49,11 @@ process RUNDBCAN_EASYCGC { 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}": diff --git a/modules/nf-core/rundbcan/easysubstrate/main.nf b/modules/nf-core/rundbcan/easysubstrate/main.nf index 812aba3e58ef..92550889c61d 100644 --- a/modules/nf-core/rundbcan/easysubstrate/main.nf +++ b/modules/nf-core/rundbcan/easysubstrate/main.nf @@ -20,7 +20,7 @@ process RUNDBCAN_EASYSUBSTRATE { 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 tuple val(meta), path("${prefix}_total_cgc_info.tsv") , emit: total_cgc_info tuple val(meta), path("${prefix}_substrate_prediction.tsv"), emit: substrate_prediction @@ -53,13 +53,15 @@ process RUNDBCAN_EASYSUBSTRATE { 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 mv CGC.faa ${prefix}_CGC.faa mv PUL_blast.out ${prefix}_PUL_blast.out mv substrate_prediction.tsv ${prefix}_substrate_prediction.tsv mv synteny_pdf/ ${prefix}_synteny_pdf/ + 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}": From 9ace581d512214592ccd75b89e12cd154c66faaa Mon Sep 17 00:00:00 2001 From: HaidYi Date: Sun, 25 Jan 2026 23:22:37 -0600 Subject: [PATCH 5/6] update snapshot --- .../cazymeannotation/tests/main.nf.test.snap | 32 +++------ .../rundbcan/easycgc/tests/main.nf.test.snap | 68 +++++++------------ .../easysubstrate/tests/main.nf.test.snap | 44 +++++------- 3 files changed, 52 insertions(+), 92 deletions(-) diff --git a/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap b/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap index 35dc98e4724d..eb85c019b247 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap +++ b/modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap @@ -93,7 +93,7 @@ { "id": "test" }, - "test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54" + "test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d" ] ], "1": [ @@ -105,30 +105,25 @@ ] ], "2": [ - [ - { - "id": "test" - }, - "test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b" - ] + ], "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": [ @@ -136,7 +131,7 @@ { "id": "test" }, - "test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84" + "test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e" ] ], "dbcanhmm_results": [ @@ -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" } } \ No newline at end of file diff --git a/modules/nf-core/rundbcan/easycgc/tests/main.nf.test.snap b/modules/nf-core/rundbcan/easycgc/tests/main.nf.test.snap index 664f76704c03..63596ffbded5 100644 --- a/modules/nf-core/rundbcan/easycgc/tests/main.nf.test.snap +++ b/modules/nf-core/rundbcan/easycgc/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54" + "test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d" ] ], "1": [ @@ -19,19 +19,14 @@ ] ], "2": [ - [ - { - "id": "test" - }, - "test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b" - ] + ], "3": [ [ { "id": "test" }, - "test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84" + "test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e" ] ], "4": [ @@ -39,7 +34,7 @@ { "id": "test" }, - "test_cgc.gff:md5,cb1bd08c0276b4a0a37540032863a0ac" + "test_cgc.gff:md5,eaf6a6435134fa64bfdff23517910ca8" ] ], "5": [ @@ -55,34 +50,29 @@ { "id": "test" }, - "test_diamond.out.tc:md5,4b9747475aaf438eede8556832060f83" + "test_diamond.out.tc:md5,be696c08c3fa3261318a347b62a5eba8" ] ], "7": [ - [ - { - "id": "test" - }, - "test_TF_hmm_results.tsv:md5,f63f2b2b3c4439304fa1c20c19cf1e99" - ] + ], "8": [ [ { "id": "test" }, - "test_STP_hmm_results.tsv:md5,e03c881b99bb7c7637ed600324816b5c" + "test_STP_hmm_results.tsv:md5,c928a0bc065ba211119ad18279499cae" ] ], "9": [ - "versions.yml:md5,98440d2e11ce6a66cf63395467603bb9" + "versions.yml:md5,d9f8b1280dda14e14d8a1edbc93e2c51" ], "cazyme_annotation": [ [ { "id": "test" }, - "test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54" + "test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d" ] ], "cgc_gff": [ @@ -90,7 +80,7 @@ { "id": "test" }, - "test_cgc.gff:md5,cb1bd08c0276b4a0a37540032863a0ac" + "test_cgc.gff:md5,eaf6a6435134fa64bfdff23517910ca8" ] ], "cgc_standard_out": [ @@ -106,7 +96,7 @@ { "id": "test" }, - "test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84" + "test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e" ] ], "dbcanhmm_results": [ @@ -118,19 +108,14 @@ ] ], "dbcansub_results": [ - [ - { - "id": "test" - }, - "test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b" - ] + ], "diamond_out_tc": [ [ { "id": "test" }, - "test_diamond.out.tc:md5,4b9747475aaf438eede8556832060f83" + "test_diamond.out.tc:md5,be696c08c3fa3261318a347b62a5eba8" ] ], "stp_hmm_results": [ @@ -138,32 +123,27 @@ { "id": "test" }, - "test_STP_hmm_results.tsv:md5,e03c881b99bb7c7637ed600324816b5c" + "test_STP_hmm_results.tsv:md5,c928a0bc065ba211119ad18279499cae" ] ], "tf_hmm_results": [ - [ - { - "id": "test" - }, - "test_TF_hmm_results.tsv:md5,f63f2b2b3c4439304fa1c20c19cf1e99" - ] + ], "versions": [ - "versions.yml:md5,98440d2e11ce6a66cf63395467603bb9" + "versions.yml:md5,d9f8b1280dda14e14d8a1edbc93e2c51" ] }, { "RUNDBCAN_EASYCGC": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-12T17:03:26.553650524" + "timestamp": "2026-01-25T23:10:13.587842985" }, "easycgc - stub": { "content": [ @@ -241,7 +221,7 @@ ] ], "9": [ - "versions.yml:md5,98440d2e11ce6a66cf63395467603bb9" + "versions.yml:md5,d9f8b1280dda14e14d8a1edbc93e2c51" ], "cazyme_annotation": [ [ @@ -316,19 +296,19 @@ ] ], "versions": [ - "versions.yml:md5,98440d2e11ce6a66cf63395467603bb9" + "versions.yml:md5,d9f8b1280dda14e14d8a1edbc93e2c51" ] }, { "RUNDBCAN_EASYCGC": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-12T17:03:30.257931353" + "timestamp": "2026-01-25T23:10:16.559195911" } } \ No newline at end of file diff --git a/modules/nf-core/rundbcan/easysubstrate/tests/main.nf.test.snap b/modules/nf-core/rundbcan/easysubstrate/tests/main.nf.test.snap index 936e94728265..320ca8691712 100644 --- a/modules/nf-core/rundbcan/easysubstrate/tests/main.nf.test.snap +++ b/modules/nf-core/rundbcan/easysubstrate/tests/main.nf.test.snap @@ -37,7 +37,7 @@ ] ], "12": [ - "versions.yml:md5,d5dd0946a8485d35c9593ca672a9387c" + "versions.yml:md5,bce39ebc65e74a66b3cc4c96a040d767" ], "2": [ [ @@ -202,20 +202,20 @@ ] ], "versions": [ - "versions.yml:md5,d5dd0946a8485d35c9593ca672a9387c" + "versions.yml:md5,bce39ebc65e74a66b3cc4c96a040d767" ] }, { "RUNDBCAN_EASYSUBSTRATE": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-12T17:05:25.261676793" + "timestamp": "2026-01-25T23:20:17.829403599" }, "easysubstrate - simplified": { "content": [ @@ -224,7 +224,7 @@ { "id": "test" }, - "test_overview.tsv:md5,73bd9acee752d61e096370d4fedfee54" + "test_overview.tsv:md5,946555b9669d8e0b1705ca512ad3c60d" ] ], [ @@ -236,19 +236,14 @@ ] ], [ - [ - { - "id": "test" - }, - "test_dbCANsub_hmm_results.tsv:md5,7ce7b6536845ffa8907b3f3fb2b77a1b" - ] + ], [ [ { "id": "test" }, - "test_diamond.out:md5,c935cda6778ca2b6aaaa4362b6f24d84" + "test_diamond.out:md5,f6d902c0af43d8b33a41d647327c673e" ] ], [ @@ -256,7 +251,7 @@ { "id": "test" }, - "test_cgc.gff:md5,cb1bd08c0276b4a0a37540032863a0ac" + "test_cgc.gff:md5,eaf6a6435134fa64bfdff23517910ca8" ] ], [ @@ -272,23 +267,18 @@ { "id": "test" }, - "test_diamond.out.tc:md5,4b9747475aaf438eede8556832060f83" + "test_diamond.out.tc:md5,be696c08c3fa3261318a347b62a5eba8" ] ], [ - [ - { - "id": "test" - }, - "test_TF_hmm_results.tsv:md5,f63f2b2b3c4439304fa1c20c19cf1e99" - ] + ], [ [ { "id": "test" }, - "test_STP_hmm_results.tsv:md5,e03c881b99bb7c7637ed600324816b5c" + "test_STP_hmm_results.tsv:md5,c928a0bc065ba211119ad18279499cae" ] ], [ @@ -296,22 +286,22 @@ { "id": "test" }, - "test_total_cgc_info.tsv:md5,0b1411698abea697723acd7be2ff03a7" + "test_total_cgc_info.tsv:md5,86b551fe09a76b253b6c955363255af9" ] ], [ - "versions.yml:md5,d5dd0946a8485d35c9593ca672a9387c" + "versions.yml:md5,bce39ebc65e74a66b3cc4c96a040d767" ], { "RUNDBCAN_EASYSUBSTRATE": { - "dbcan": "5.1.2" + "dbcan": "5.2.4" } } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-12T17:05:21.376354173" + "timestamp": "2026-01-25T23:20:14.786535208" } } \ No newline at end of file From f4590a15b5cb017d182ac4bfc0dae9a5d26d8985 Mon Sep 17 00:00:00 2001 From: HaidYi Date: Wed, 28 Jan 2026 09:30:52 -0600 Subject: [PATCH 6/6] update to 5.2.5 --- modules/nf-core/rundbcan/cazymeannotation/main.nf | 2 +- modules/nf-core/rundbcan/database/main.nf | 2 +- modules/nf-core/rundbcan/easycgc/main.nf | 2 +- modules/nf-core/rundbcan/easysubstrate/main.nf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/rundbcan/cazymeannotation/main.nf b/modules/nf-core/rundbcan/cazymeannotation/main.nf index ba70f6e171de..ce6a36381544 100644 --- a/modules/nf-core/rundbcan/cazymeannotation/main.nf +++ b/modules/nf-core/rundbcan/cazymeannotation/main.nf @@ -5,7 +5,7 @@ process RUNDBCAN_CAZYMEANNOTATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : - 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" + 'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data) diff --git a/modules/nf-core/rundbcan/database/main.nf b/modules/nf-core/rundbcan/database/main.nf index 7b784613eff3..bdc3a2f149b1 100644 --- a/modules/nf-core/rundbcan/database/main.nf +++ b/modules/nf-core/rundbcan/database/main.nf @@ -4,7 +4,7 @@ process RUNDBCAN_DATABASE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : - 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" + 'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }" output: path "dbcan_db" , emit: dbcan_db diff --git a/modules/nf-core/rundbcan/easycgc/main.nf b/modules/nf-core/rundbcan/easycgc/main.nf index 827d026b9395..7934b036edb1 100644 --- a/modules/nf-core/rundbcan/easycgc/main.nf +++ b/modules/nf-core/rundbcan/easycgc/main.nf @@ -5,7 +5,7 @@ process RUNDBCAN_EASYCGC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : - 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" + 'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data) diff --git a/modules/nf-core/rundbcan/easysubstrate/main.nf b/modules/nf-core/rundbcan/easysubstrate/main.nf index 92550889c61d..06b381da20cd 100644 --- a/modules/nf-core/rundbcan/easysubstrate/main.nf +++ b/modules/nf-core/rundbcan/easysubstrate/main.nf @@ -5,7 +5,7 @@ process RUNDBCAN_EASYSUBSTRATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dbcan:5.2.4--pyhdfd78af_0' : - 'biocontainers/dbcan:5.2.4--pyhdfd78af_0' }" + 'biocontainers/dbcan:5.2.5--pyhdfd78af_0' }" input: tuple val(meta), path(input_raw_data)