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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.1.1") | ||
| addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.9") | ||
| addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.1.0") | ||
| addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.9.0") |
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2 changes: 1 addition & 1 deletion
2
src/main/resources/io/viash/runners/nextflow/arguments/_processInputValues.nf
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154 changes: 154 additions & 0 deletions
154
src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| def publishFiles(Map args) { | ||
| def key_ = args.get("key") | ||
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| assert key_ != null : "publishFiles: key must be specified" | ||
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| workflow publishFilesWf { | ||
| take: input_ch | ||
| main: | ||
| input_ch | ||
| | map { tup -> | ||
| def id_ = tup[0] | ||
| def state_ = tup[1] | ||
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| // the input files and the target output filenames | ||
| def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose() | ||
| def inputFiles_ = inputoutputFilenames_[0] | ||
| def outputFilenames_ = inputoutputFilenames_[1] | ||
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| [id_, inputFiles_, outputFilenames_] | ||
| } | ||
| | publishFilesProc | ||
| emit: input_ch | ||
| } | ||
| return publishFilesWf | ||
| } | ||
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| process publishFilesProc { | ||
| // todo: check publishpath? | ||
| publishDir path: "${getPublishDir()}/", mode: "copy" | ||
| tag "$id" | ||
| input: | ||
| tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) | ||
| output: | ||
| tuple val(id), path{outputFiles} | ||
| script: | ||
| def copyCommands = [ | ||
| inputFiles instanceof List ? inputFiles : [inputFiles], | ||
| outputFiles instanceof List ? outputFiles : [outputFiles] | ||
| ] | ||
| .transpose() | ||
| .collectMany{infile, outfile -> | ||
| if (infile.toString() != outfile.toString()) { | ||
| [ | ||
| "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"", | ||
| "cp -r '${infile.toString()}' '${outfile.toString()}'" | ||
| ] | ||
| } else { | ||
| // no need to copy if infile is the same as outfile | ||
| [] | ||
| } | ||
| } | ||
| """ | ||
| echo "Copying output files to destination folder" | ||
| ${copyCommands.join("\n ")} | ||
| """ | ||
| } | ||
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| // this assumes that the state contains no other values other than those specified in the config | ||
| def publishFilesByConfig(Map args) { | ||
| def config = args.get("config") | ||
| assert config != null : "publishFilesByConfig: config must be specified" | ||
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| def key_ = args.get("key", config.name) | ||
| assert key_ != null : "publishFilesByConfig: key must be specified" | ||
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| workflow publishFilesSimpleWf { | ||
| take: input_ch | ||
| main: | ||
| input_ch | ||
| | map { tup -> | ||
| def id_ = tup[0] | ||
| def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] | ||
| def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] | ||
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| // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where | ||
| // - key is a String | ||
| // - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path) | ||
| // - inputPath is a List[Path] | ||
| // - outputFilename is a List[String] | ||
| // - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml) | ||
| def processedState = | ||
| config.allArguments | ||
| .findAll { it.direction == "output" } | ||
| .collectMany { par -> | ||
| def plainName_ = par.plainName | ||
| // if the state does not contain the key, it's an | ||
| // optional argument for which the component did | ||
| // not generate any output OR multiple channels were emitted | ||
| // and the output was just not added to using the channel | ||
| // that is now being parsed | ||
| if (!state_.containsKey(plainName_)) { | ||
| return [] | ||
| } | ||
| def value = state_[plainName_] | ||
| // if the parameter is not a file, it should be stored | ||
| // in the state as-is, but is not something that needs | ||
| // to be copied from the source path to the dest path | ||
| if (par.type != "file") { | ||
| return [[inputPath: [], outputFilename: []]] | ||
| } | ||
| // if the orig state does not contain this filename, | ||
| // it's an optional argument for which the user specified | ||
| // that it should not be returned as a state | ||
| if (!origState_.containsKey(plainName_)) { | ||
| return [] | ||
| } | ||
| def filenameTemplate = origState_[plainName_] | ||
| // if the pararameter is multiple: true, fetch the template | ||
| if (par.multiple && filenameTemplate instanceof List) { | ||
| filenameTemplate = filenameTemplate[0] | ||
| } | ||
| // instantiate the template | ||
| def filename = filenameTemplate | ||
| .replaceAll('\\$id', id_) | ||
| .replaceAll('\\$\\{id\\}', id_) | ||
| .replaceAll('\\$key', key_) | ||
| .replaceAll('\\$\\{key\\}', key_) | ||
| if (par.multiple) { | ||
| // if the parameter is multiple: true, the filename | ||
| // should contain a wildcard '*' that is replaced with | ||
| // the index of the file | ||
| assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" | ||
| def outputPerFile = value.withIndex().collect{ val, ix -> | ||
| def filename_ix = filename.replace("*", ix.toString()) | ||
| def inputPath = val instanceof File ? val.toPath() : val | ||
| [inputPath: inputPath, outputFilename: filename_ix] | ||
| } | ||
| def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> | ||
| [key, outputPerFile.collect{dic -> dic[key]}] | ||
| } | ||
| return [[key: plainName_] + transposedOutputs] | ||
| } else { | ||
| def value_ = java.nio.file.Paths.get(filename) | ||
| def inputPath = value instanceof File ? value.toPath() : value | ||
| return [[inputPath: [inputPath], outputFilename: [filename]]] | ||
| } | ||
| } | ||
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| def inputPaths = processedState.collectMany{it.inputPath} | ||
| def outputFilenames = processedState.collectMany{it.outputFilename} | ||
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| [id_, inputPaths, outputFilenames] | ||
| } | ||
| | publishFilesProc | ||
| emit: input_ch | ||
| } | ||
| return publishFilesSimpleWf | ||
| } | ||
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