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split2 #378

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8 changes: 4 additions & 4 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ process {
//
withName : MUMMER {
ext.args = "-n -b -c -L -l 400"
ext.prefix = { "${meta.rid}_VS_${meta.qid}" }
ext.prefix = { "${meta.id}" }
}


Expand Down Expand Up @@ -233,13 +233,13 @@ process {
}

withName: ".*:.*:SELFCOMP:SEQKIT_SPLIT_REF" {
ext.args = ""
ext.args = { " -p ${meta.cn} --by-part-prefix ref_chunk --out-dir refchunks "}
ext.prefix = { "${meta.id}_ref" }
}

withName: ".*:.*:SELFCOMP:SEQKIT_SPLIT_QUERY" {
ext.args = ""
ext.prefix = { "${meta.id}_query" }
ext.args = { " -p ${meta.cn} --by-part-prefix query_chunk --out-dir querychunks "}
ext.prefix = { "${meta.id}_ref" }
}

//
Expand Down
162 changes: 123 additions & 39 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,199 +8,283 @@
"bedtools/bamtobed": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/makewindows": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/map": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/sort": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"busco/busco": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/busco/busco/busco-busco.diff"
},
"bwamem2/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cat/cat": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cooler/cload": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cooler/zoomify": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
},
"fastk/fastk": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
},
"gnu/sort": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"merquryfk/merquryfk": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
},
"minimap2/align": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
},
"minimap2/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"miniprot/align": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"miniprot/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"mummer": {
"branch": "master",
"git_sha": "a15872dde4c4affaac2dfee6c3c65fadab4719bd",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"paftools/sam2paf": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"pretextmap": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/pretextmap/pretextmap.diff"
},
"pretextsnapshot": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff"
},
"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/markdup": {
"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": "669eb24fd82a9d3cb18ad0e73673ecb26827f683",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"seqkit/split2": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": [
"modules"
],
"patch": "modules/nf-core/seqkit/split2/seqkit-split2.diff"
},
"seqtk/cutn": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ucsc/bedtobigbed": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"windowmasker/mkcounts": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"windowmasker/ustat": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"yahs": {
"branch": "master",
"git_sha": "d3a3d04073af68437f07e0fb9b88aa6172c3f678",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
},
Expand All @@ -209,4 +293,4 @@
}
}
}
}
}
44 changes: 0 additions & 44 deletions modules/local/seqkit/split/main.nf
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