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@luisas
luisas committed Dec 13, 2023
1 parent 851303b commit 2de221e
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -27,6 +27,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
[#54](https://github.com/nf-core/multiplesequencealign/issues/54) - Update modules versions from nf-core tools.
[#80](https://github.com/nf-core/multiplesequencealign/pull/80) - Update modules versions from nf-core tools with nf-test.
[#32](https://github.com/nf-core/multiplesequencealign/issues/32) - Update Stats workflow with nf-core modules for merging.
[#81](https://github.com/nf-core/multiplesequencealign/pull/81) - Update Eval workflow with nf-core modules for merging.

### `Dependencies`

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12 changes: 6 additions & 6 deletions conf/modules.config
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Expand Up @@ -104,7 +104,7 @@ process {
path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1]}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
]
}

withName: 'TCOFFEE_ALNCOMPARE_TC'{
Expand All @@ -114,7 +114,7 @@ process {
path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1]}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
]
}

withName: 'TCOFFEE_IRMSD'{
Expand All @@ -123,7 +123,7 @@ process {
path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1]}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
]
}

withName: 'PARSE_IRMSD'{
Expand All @@ -132,7 +132,7 @@ process {
path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1]}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
]
}

withName: "CONCAT_SEQSTATS"{
Expand All @@ -152,7 +152,7 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: "CONCAT_TC"{
ext.prefix = { "summary_tc" }
publishDir = [
Expand All @@ -161,7 +161,7 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: "CONCAT_IRMSD"{
ext.prefix = { "summary_irmsd" }
publishDir = [
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78 changes: 20 additions & 58 deletions modules.json
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Expand Up @@ -8,138 +8,100 @@
"clustalo/align": {
"branch": "master",
"git_sha": "1a8cc5bb3ea3348c552abb23fb380a6390fc0666",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"clustalo/guidetree": {
"branch": "master",
"git_sha": "1f253ec05723293df7757af8769f8389b7a1884e",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"csvtk/concat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"csvtk/join": {
"branch": "master",
"git_sha": "b2420a8bbd8af137380aa0a0c2e9a92456e5bb21",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"famsa/align": {
"branch": "master",
"git_sha": "36fc6f7dfc7bf0b4226681df58486ab1948f7df2",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"famsa/guidetree": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"kalign/align": {
"branch": "master",
"git_sha": "899b6b2f3e91eb0620458131fed1373c82f18ff1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"learnmsa/align": {
"branch": "master",
"git_sha": "7ca2d77c844e4d0272da08f2ff56ce5cac14e456",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"mafft": {
"branch": "master",
"git_sha": "c0a22acfb0accdf8ab3ea4f755a4865d538dc53f",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"muscle5/super5": {
"branch": "master",
"git_sha": "f883758bfbfd0dea01013750581d378e8c98aafc",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"tcoffee/align": {
"branch": "master",
"git_sha": "c83c78835ca6d7a55b3f200718d887cbc7149d37",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"tcoffee/alncompare": {
"branch": "master",
"git_sha": "74ee27ccbc2a492a8479323b212b2a42317c3109",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"tcoffee/irmsd": {
"branch": "master",
"git_sha": "5074bd37c59454497e790d9210e2f7a876f2c24f",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"tcoffee/seqreformat": {
"branch": "master",
"git_sha": "f759fd45ecabb40c761df1338a4bb3851171a7f7",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"zip": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
}
}
}
}
}
}
}
2 changes: 1 addition & 1 deletion modules/local/parse_irmsd.nf
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Expand Up @@ -18,7 +18,7 @@ process PARSE_IRMSD {
def values = meta.values().join(",")
"""
# Parse irmsd file
grep "TOTAL" $infile > ${prefix}.total_irmsd
grep "TOTAL" $infile > ${prefix}.total_irmsd
parsers.py -i ${prefix}.total_irmsd -o ${prefix}.scores.csv
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