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Example changes how to stage inputs/output modules in a more 'nextflowy' way #1

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Example changes how to stage inputs/output modules in a more 'nextflowy' way #1

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b14fa0d
Example changes how to stage inputs/outputs in a more 'nextflowy' way
jfy133 Dec 2, 2025
d0fc776
Also publish the tmp_Dir
jfy133 Dec 2, 2025
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10 changes: 9 additions & 1 deletion conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,14 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h',
]
}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
Expand All @@ -20,5 +28,5 @@ params {

// Input data
files = 'MAGFlow/data/*'

}
50 changes: 37 additions & 13 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,53 +8,71 @@
"busco/busco": {
"branch": "master",
"git_sha": "17486961b8b1ab1aae258c83a7e947b40d8ab670",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/busco/busco/busco-busco.diff"
},
"checkm2/databasedownload": {
"branch": "master",
"git_sha": "1bfd681e88ef66c037b3ffd6571ab00370230c7b",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/checkm2/databasedownload/checkm2-databasedownload.diff"
},
"checkm2/predict": {
"branch": "master",
"git_sha": "1bfd681e88ef66c037b3ffd6571ab00370230c7b",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/checkm2/predict/checkm2-predict.diff"
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gtdbtk/classifywf": {
"branch": "master",
"git_sha": "28a811586021f5c81639355c1fe4a6651a07ab17",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/gtdbtk/classifywf/gtdbtk-classifywf.diff"
},
"gunc/downloaddb": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/gunc/downloaddb/gunc-downloaddb.diff"
},
"gunc/run": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/gunc/run/gunc-run.diff"
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"quast": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/quast/quast.diff"
}
}
Expand All @@ -64,20 +82,26 @@
"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"
]
}
}
}
}
}
}
}
61 changes: 37 additions & 24 deletions modules/nf-core/checkm2/predict/checkm2-predict.diff
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32 changes: 15 additions & 17 deletions modules/nf-core/checkm2/predict/main.nf
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