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Refactor for publishing #7

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Merged
mwang87 merged 7 commits into from
Jun 20, 2025
Merged

Refactor for publishing #7

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63a8d38
bug fix
mwang87 Jun 20, 2025
e1661f5
compatiblity
mwang87 Jun 20, 2025
72d7d1d
updating
mwang87 Jun 20, 2025
bf297e2
updating
mwang87 Jun 20, 2025
6658392
updating
mwang87 Jun 20, 2025
6b48d47
using new modules
mwang87 Jun 20, 2025
15ed0a9
bump version
mwang87 Jun 20, 2025
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14 changes: 12 additions & 2 deletions nf_workflow.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,23 @@ nextflow.enable.dsl=2
params.input_spectra = "$baseDir/data/"

//This publish dir is mostly useful when we want to import modules in other workflows, keep it here usually don't change it
params.publishdir = "$baseDir/nf_output"
params.publishdir = "$launchDir"
TOOL_FOLDER = "$moduleDir/bin"
MODULES_FOLDER = "$TOOL_FOLDER/NextflowModules"

// A lot of useful modules are already implemented and added to the nextflow modules, you can import them to use
include {summaryLibrary} from "$MODULES_FOLDER/nf_library_search_modules.nf" addParams(publishDir: params.publishdir)
// the publishdir is a key word that we're using around all our modules to control where the output files will be saved
include {summaryLibrary} from "$MODULES_FOLDER/nf_library_search_modules.nf" addParams(publishdir: params.publishdir)

// COMPATIBILITY NOTE: The following might be necessary if this workflow is being deployed in a slightly different environemnt
// checking if outdir is defined,
// if so, then set publishdir to outdir
if (params.outdir) {
params.publishdir = params.outdir
}

// Augmenting with nf_output
params.publishdir = "${params.publishdir}/nf_output"

process processDataPython {
/* This is a sample process that runs a python script.
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