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Interproscan #104

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merged 13 commits into from
Jan 12, 2024
Merged

Interproscan #104

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52ca25f
replace local interproscan module with nf-core module
MartinPippel Jan 11, 2024
0a972be
replace local interproscan module with nf-core module
MartinPippel Jan 11, 2024
a9d24f1
Update subworkflows/functional_annotation/main.nf
MartinPippel Jan 11, 2024
ca4d3bc
Update subworkflows/functional_annotation/README.md
MartinPippel Jan 11, 2024
f2074ae
remove unnecessary aguments -dp and -f as well as cpus
MartinPippel Jan 11, 2024
8ac0587
remove unnecessary argument cpus
MartinPippel Jan 11, 2024
e0b631c
add cpu=8 by default, add -dra option for speed up (residue annotatio…
MartinPippel Jan 11, 2024
fc17085
get rid of predefined applications
MartinPippel Jan 11, 2024
a3ceb60
create patch for interproscan -appl argument
MartinPippel Jan 11, 2024
f8239af
Revert "add cpu=8 by default, add -dra option for speed up (residue a…
MartinPippel Jan 12, 2024
21f2267
add default cpu = 2 to test config
MartinPippel Jan 12, 2024
89a7330
revert back to use -appl option, because otherwise the pipeline crashes
MartinPippel Jan 12, 2024
e368916
remove obsolete interproscan path
MartinPippel Jan 12, 2024
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2 changes: 0 additions & 2 deletions config/functional_annotation_modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,9 @@ process {
}
withName: 'INTERPROSCAN' {
ext.args = [
'-f TSV',
'--iprlookup',
'--goterms',
'-pa',
'-dp',
'-t p'
].join(' ').trim()
}
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3 changes: 1 addition & 2 deletions config/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,11 @@ if ( params.subworkflow == 'functional_annotation' ) {
}
process {
withName: 'FUNCTIONAL_ANNOTATION:INTERPROSCAN' {
cpus = 2
ext.args = [
'-f TSV',
// '--iprlookup',
// '--goterms',
// '-pa',
// '-dp',
'-t p'
].join(' ').trim()
}
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91 changes: 54 additions & 37 deletions modules.json
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@@ -1,41 +1,58 @@
{
"name": "NBIS Genome Annotation Workflow",
"homePage": "",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"blast/makeblastdb": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
},
"busco": {
"branch": "master",
"git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": ["modules"]
}
"name": "NBIS Genome Annotation Workflow",
"homePage": "",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"blast/makeblastdb": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
],
"patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
},
"busco": {
"branch": "master",
"git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
"installed_by": [
"modules"
]
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
"installed_by": [
"modules"
]
},
"interproscan": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": [
"modules"
]
}
}
},
"subworkflows": {
"nf-core": {}
}
}
},
"subworkflows": {
"nf-core": {}
}
}
}
}
34 changes: 0 additions & 34 deletions modules/local/interproscan.nf
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7 changes: 7 additions & 0 deletions modules/nf-core/interproscan/environment.yml
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88 changes: 88 additions & 0 deletions modules/nf-core/interproscan/main.nf
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54 changes: 54 additions & 0 deletions modules/nf-core/interproscan/meta.yml
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65 changes: 65 additions & 0 deletions modules/nf-core/interproscan/tests/main.nf.test
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