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Seqkit replace - fix #9647 and #9646 #12213

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Seqkit replace - fix #9647 and #9646 #12213

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2c45c10
output name is unique to avoid input/output name clash
ammaraziz Jul 1, 2026
eb40843
update snap
ammaraziz Jul 1, 2026
d39e175
Merge branch 'master' into seqkit-update
ammaraziz Jul 2, 2026
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4 changes: 2 additions & 2 deletions modules/nf-core/seqkit/replace/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ process SEQKIT_REPLACE {

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}_replaced"
def extension = "fastq"
if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.faa|.+\.faa.gz/) {
extension = "fasta"
Expand All @@ -35,7 +35,7 @@ process SEQKIT_REPLACE {
replace \\
${args} \\
--threads ${task.cpus} \\
-i ${fastx} \\
${fastx} \\
-o ${prefix}.${endswith}
"""

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18 changes: 9 additions & 9 deletions modules/nf-core/seqkit/replace/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
{
"id": "test"
},
"test.fasta:md5,b1518908253a4997fcad98270751112e"
"test_replaced.fasta:md5,b1518908253a4997fcad98270751112e"
]
],
"versions_seqkit": [
Expand All @@ -45,10 +45,10 @@
]
}
],
"timestamp": "2026-06-12T17:26:01.449665395",
"timestamp": "2026-07-01T17:34:12.934060454",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
"nextflow": "26.04.4"
}
},
"sarscov2 - fasta - uncomp - custom": {
Expand All @@ -59,7 +59,7 @@
{
"id": "test"
},
"test.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
"test_replaced.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
]
],
"versions_seqkit": [
Expand All @@ -71,10 +71,10 @@
]
}
],
"timestamp": "2026-06-13T12:54:19.323281146",
"timestamp": "2026-07-01T17:34:18.009100471",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
"nextflow": "26.04.4"
}
},
"sarscov2 - fasta - replace": {
Expand All @@ -85,7 +85,7 @@
{
"id": "test"
},
"test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
"test_replaced.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
]
],
"versions_seqkit": [
Expand All @@ -97,10 +97,10 @@
]
}
],
"timestamp": "2026-06-12T17:25:54.471016576",
"timestamp": "2026-07-01T17:34:07.395747978",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
"nextflow": "26.04.4"
}
}
}