diff --git a/.nf-core.yml b/.nf-core.yml
index fcc8054..306897d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -12,8 +12,7 @@ nf_core_version: 3.5.1
repository_type: pipeline
template:
author: Olga Botvinnik
- description: The best protein annotation pipeline in the world. Protein fasta ->
- ??? -> Annotations!
+ description: Generation of sequence-level annotations for amino acid sequences
version: 1.0.0dev
force: true
outdir: .
diff --git a/assets/email_template.html b/assets/email_template.html
index faeae5f..6918b57 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -4,7 +4,7 @@
-
+
nf-core/proteinannotator Pipeline Report
diff --git a/modules.json b/modules.json
index 3c9fb89..37ba5b8 100644
--- a/modules.json
+++ b/modules.json
@@ -37,7 +37,7 @@
},
"seqkit/replace": {
"branch": "master",
- "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+ "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
"installed_by": ["faa_seqfu_seqkit"]
},
"seqkit/rmdup": {
@@ -52,7 +52,7 @@
},
"seqkit/stats": {
"branch": "master",
- "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+ "git_sha": "28935b89b7e1f19e835f8c6e4c8322d4b505dded",
"installed_by": ["modules"]
},
"untar": {
@@ -66,7 +66,7 @@
"nf-core": {
"faa_seqfu_seqkit": {
"branch": "master",
- "git_sha": "911a3c360b0ebdae4e36beaf734e6905174d3507",
+ "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index bca584f..dd03dac 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -12,7 +12,7 @@ process SEQKIT_REPLACE {
output:
tuple val(meta), path("*.fast*"), emit: fastx
- path "versions.yml", emit: versions
+ tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/seqkit v//'"), emit: versions_seqkit, topic: versions
when:
task.ext.when == null || task.ext.when
@@ -36,11 +36,6 @@ process SEQKIT_REPLACE {
--threads ${task.cpus} \\
-i ${fastx} \\
-o ${prefix}.${endswith}
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- seqkit: \$( seqkit version | sed 's/seqkit v//' )
- END_VERSIONS
"""
stub:
@@ -53,10 +48,5 @@ process SEQKIT_REPLACE {
"""
echo "" | gzip > ${prefix}.${endswith}
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- seqkit: \$( seqkit version | sed 's/seqkit v//' )
- END_VERSIONS
"""
}
diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml
index 6d79e38..1592787 100644
--- a/modules/nf-core/seqkit/replace/meta.yml
+++ b/modules/nf-core/seqkit/replace/meta.yml
@@ -40,13 +40,29 @@ output:
pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
+ versions_seqkit:
+ - - ${task.process}:
+ type: string
+ description: The name of the process
+ - seqkit:
+ type: string
+ description: The name of the tool
+ - "seqkit version | sed 's/seqkit v//'":
+ type: eval
+ description: The expression to obtain the version of seqkit
+
+topics:
versions:
- - versions.yml:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
- ontologies:
- - edam: http://edamontology.org/format_3750 # YAML
+ - - ${task.process}:
+ type: string
+ description: The name of the process
+ - seqkit:
+ type: string
+ description: The name of the tool
+ - "seqkit version | sed 's/seqkit v//'":
+ type: eval
+ description: The expression to obtain the version of seqkit
+
authors:
- "@mjcipriano"
maintainers:
diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
index 62bcecd..fdae3eb 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
@@ -11,7 +11,11 @@
]
],
"1": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
],
"fastx": [
[
@@ -21,16 +25,20 @@
"test.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
- "versions": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ "versions_seqkit": [
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:10:45.336609"
+ "timestamp": "2026-02-03T14:51:31.369966565"
},
"sarscov2 - fasta - replace - uncompressed": {
"content": [
@@ -44,7 +52,11 @@
]
],
"1": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
],
"fastx": [
[
@@ -54,16 +66,20 @@
"test.fasta:md5,b1518908253a4997fcad98270751112e"
]
],
- "versions": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ "versions_seqkit": [
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-23T11:36:29.526831467"
+ "timestamp": "2026-02-03T14:51:20.851601162"
},
"sarscov2 - fasta - uncomp - custom": {
"content": [
@@ -77,7 +93,11 @@
]
],
"1": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
],
"fastx": [
[
@@ -87,16 +107,20 @@
"test..fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
]
],
- "versions": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ "versions_seqkit": [
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-23T11:36:34.791793064"
+ "timestamp": "2026-02-03T14:51:26.121667583"
},
"sarscov2 - fasta - replace": {
"content": [
@@ -110,7 +134,11 @@
]
],
"1": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
],
"fastx": [
[
@@ -120,15 +148,19 @@
"test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
]
],
- "versions": [
- "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
+ "versions_seqkit": [
+ [
+ "SEQKIT_REPLACE",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-23T11:36:24.47433864"
+ "timestamp": "2026-02-03T14:51:15.520168225"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf
index f69fcb6..540aa88 100644
--- a/modules/nf-core/seqkit/stats/main.nf
+++ b/modules/nf-core/seqkit/stats/main.nf
@@ -12,7 +12,7 @@ process SEQKIT_STATS {
output:
tuple val(meta), path("*.tsv"), emit: stats
- path "versions.yml", emit: versions
+ tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/seqkit v//'"), emit: versions_seqkit, topic: versions
when:
task.ext.when == null || task.ext.when
@@ -26,21 +26,11 @@ process SEQKIT_STATS {
--threads ${task.cpus} \\
${args} \\
${reads} > '${prefix}.tsv'
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- seqkit: \$( seqkit version | sed 's/seqkit v//' )
- END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- seqkit: \$( seqkit version | sed 's/seqkit v//' )
- END_VERSIONS
"""
}
diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml
index 172581b..1d51b05 100644
--- a/modules/nf-core/seqkit/stats/meta.yml
+++ b/modules/nf-core/seqkit/stats/meta.yml
@@ -41,13 +41,29 @@ output:
pattern: "*.tsv"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV
+ versions_seqkit:
+ - - ${task.process}:
+ type: string
+ description: The name of the process
+ - seqkit:
+ type: string
+ description: The name of the tool
+ - "seqkit version | sed 's/seqkit v//'":
+ type: eval
+ description: The expression to obtain the version of seqkit
+
+topics:
versions:
- - versions.yml:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
- ontologies:
- - edam: http://edamontology.org/format_3750 # YAML
+ - - ${task.process}:
+ type: string
+ description: The name of the process
+ - seqkit:
+ type: string
+ description: The name of the tool
+ - "seqkit version | sed 's/seqkit v//'":
+ type: eval
+ description: The expression to obtain the version of seqkit
+
authors:
- "@Midnighter"
- "@heuermh"
diff --git a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap b/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
index 6ce5911..b83e6a6 100644
--- a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -23,16 +27,20 @@
"test.tsv:md5,14f97a9e0414998854ead651e0e69449"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:09.132477"
+ "timestamp": "2026-02-03T13:29:39.937621054"
},
"genome_fasta": {
"content": [
@@ -47,7 +55,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -58,16 +70,20 @@
"test.tsv:md5,82b33df8ec2515560b80c3d0bc64c898"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:13.678978"
+ "timestamp": "2026-02-03T13:29:45.268086738"
},
"transcriptome_fasta": {
"content": [
@@ -82,7 +98,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -93,16 +113,20 @@
"test.tsv:md5,eef67c2e2f225391836d59d5b0d6c3b7"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:18.204844"
+ "timestamp": "2026-02-03T13:29:50.657274211"
},
"single_end": {
"content": [
@@ -117,7 +141,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -128,16 +156,20 @@
"test.tsv:md5,f172827a8608b646559cc39c6ca05085"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:00.240123"
+ "timestamp": "2026-02-03T13:29:29.264287187"
},
"paired_end": {
"content": [
@@ -152,7 +184,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -163,16 +199,20 @@
"test.tsv:md5,f172827a8608b646559cc39c6ca05085"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:04.668822"
+ "timestamp": "2026-02-03T13:29:34.665600897"
},
"single_end - stub": {
"content": [
@@ -187,7 +227,11 @@
]
],
"1": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
],
"stats": [
[
@@ -198,15 +242,19 @@
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
- "versions": [
- "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
+ "versions_seqkit": [
+ [
+ "SEQKIT_STATS",
+ "seqkit",
+ "2.9.0"
+ ]
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "24.10.3"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-01-15T15:35:22.85489"
+ "timestamp": "2026-02-03T13:29:55.952952629"
}
}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index e4e5ca7..ef821b5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -283,7 +283,7 @@ manifest {
]
]
homePage = 'https://github.com/nf-core/proteinannotator'
- description = """The best protein annotation pipeline in the world. Protein fasta -> ??? -> Annotations!"""
+ description = """Generation of sequence-level annotations for amino acid sequences"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.10.0'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 836a843..2e10e83 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -2,7 +2,7 @@
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/proteinannotator/master/nextflow_schema.json",
"title": "nf-core/proteinannotator pipeline parameters",
- "description": "The best protein annotation pipeline in the world. Protein fasta -> ??? -> Annotations!",
+ "description": "Generation of sequence-level annotations for amino acid sequences",
"type": "object",
"$defs": {
"input_output_options": {
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
index 380d636..068e658 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
@@ -23,7 +23,6 @@ workflow FAA_SEQFU_SEQKIT {
ch_versions = ch_versions.mix( SEQKIT_SEQ.out.versions )
SEQKIT_REPLACE( SEQKIT_SEQ.out.fastx )
- ch_versions = ch_versions.mix( SEQKIT_REPLACE.out.versions )
SEQKIT_RMDUP( SEQKIT_REPLACE.out.fastx )
ch_fasta = SEQKIT_RMDUP.out.fastx
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
index 396a1ac..b3559a3 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
@@ -27,7 +27,6 @@
"2": [
"versions.yml:md5,4a72093d798cac55be5088015708d471",
"versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
- "versions.yml:md5,8875daf0c5eea186e4b95d77bfc12d5d",
"versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
"versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
],
@@ -56,7 +55,6 @@
"versions": [
"versions.yml:md5,4a72093d798cac55be5088015708d471",
"versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
- "versions.yml:md5,8875daf0c5eea186e4b95d77bfc12d5d",
"versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
"versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
]
@@ -72,11 +70,6 @@
"seqkit": "v2.9.0"
}
},
- {
- "FAA_SEQFU_SEQKIT:SEQKIT_REPLACE": {
- "seqkit": "2.9.0"
- }
- },
{
"FAA_SEQFU_SEQKIT:SEQFU_STATS_BEFORE": {
"seqfu": "1.22.3"
@@ -90,10 +83,10 @@
]
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "25.04.7"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-09-25T12:09:29.612482377"
+ "timestamp": "2026-02-03T14:51:50.251419053"
},
"faa": {
"content": [
@@ -123,7 +116,6 @@
"2": [
"versions.yml:md5,4a72093d798cac55be5088015708d471",
"versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
- "versions.yml:md5,8875daf0c5eea186e4b95d77bfc12d5d",
"versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
"versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
],
@@ -152,16 +144,15 @@
"versions": [
"versions.yml:md5,4a72093d798cac55be5088015708d471",
"versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
- "versions.yml:md5,8875daf0c5eea186e4b95d77bfc12d5d",
"versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
"versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
]
}
],
"meta": {
- "nf-test": "0.9.2",
- "nextflow": "25.04.7"
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.3"
},
- "timestamp": "2025-09-25T12:13:23.81494802"
+ "timestamp": "2026-02-03T14:51:43.056425196"
}
}
\ No newline at end of file