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Updating modules and fixing blast_lineage bug
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@DLBPointon
DLBPointon committed Nov 21, 2024
1 parent cee7a3c commit fa27ff0
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Showing 20 changed files with 918 additions and 809 deletions.
2 changes: 1 addition & 1 deletion conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ process {

withName: 'MINIMAP2_ALIGN_SE' {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 70 : Math.ceil( ( reference.size() / 1e+9 ) * 50 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
memory = { check_max( 2.GB * ( reference.size() < 2e9 ? 70 : Math.ceil( ( reference.size() / 1e+9 ) * 50 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
time = { check_max( 10.h * task.attempt, 'time' ) }
}

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102 changes: 27 additions & 75 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,151 +8,109 @@
"blast/blastn": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"blast/makeblastdb": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
],
"installed_by": ["modules"],
"patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": [
"modules"
],
"installed_by": ["modules"],
"patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
},
"diamond/blastx": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": [
"modules"
]
"git_sha": "21f230b8cca43755bf73470e6fd0290832a98aef",
"installed_by": ["modules"]
},
"fcs/fcsadaptor": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fcs/fcsgx": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"gnu/sort": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"minimap2/align": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"minimap2/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": [
"modules"
]
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"installed_by": ["modules"]
},
"ncbitools/vecscreen": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/depth": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/view": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"seqkit/sliding": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"tiara/tiara": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
}
}
},
Expand All @@ -161,26 +119,20 @@
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
}
}
}
}
}
}
}
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