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Merge pull request #556 from viash-io/develop
Viash 0.8.0-RC3
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,6 @@ | ||
| name := "viash" | ||
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| version := "0.8.0-RC2" | ||
| version := "0.8.0-RC3" | ||
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| scalaVersion := "2.13.10" | ||
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20 changes: 20 additions & 0 deletions
20
src/main/resources/io/viash/platforms/nextflow/arguments/_processInputValues.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| Map _processInputValues(Map inputs, Map config, String id, String key) { | ||
| if (!workflow.stubRun) { | ||
| config.functionality.allArguments.each { arg -> | ||
| if (arg.required) { | ||
| assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : | ||
| "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing" | ||
| } | ||
| } | ||
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| inputs = inputs.collectEntries { name, value -> | ||
| def par = config.functionality.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } | ||
| assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument" | ||
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| value = _checkArgumentType("input", par, value, id, key) | ||
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| [ name, value ] | ||
| } | ||
| } | ||
| return inputs | ||
| } |
20 changes: 20 additions & 0 deletions
20
src/main/resources/io/viash/platforms/nextflow/arguments/_processOutputValues.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| Map _processOutputValues(Map outputs, Map config, String id, String key) { | ||
| if (!workflow.stubRun) { | ||
| config.functionality.allArguments.each { arg -> | ||
| if (arg.direction == "output" && arg.required) { | ||
| assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : | ||
| "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing" | ||
| } | ||
| } | ||
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| outputs = outputs.collectEntries { name, value -> | ||
| def par = config.functionality.allArguments.find { it.plainName == name && it.direction == "output" } | ||
| assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument" | ||
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| value = _checkArgumentType("output", par, value, id, key) | ||
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| [ name, value ] | ||
| } | ||
| } | ||
| return outputs | ||
| } |
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105 changes: 105 additions & 0 deletions
105
src/main/resources/io/viash/platforms/nextflow/channel/runEach.nf
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,105 @@ | ||
| /** | ||
| * Run a list of components on a stream of data. | ||
| * | ||
| * @param components: list of Viash VDSL3 modules to run | ||
| * @param fromState: a closure, a map or a list of keys to extract from the input data. | ||
| * If a closure, it will be called with the id, the data and the component itself. | ||
| * @param toState: a closure, a map or a list of keys to extract from the output data | ||
| * If a closure, it will be called with the id, the output data, the old state and the component itself. | ||
| * @param filter: filter function to apply to the input. | ||
| * It will be called with the id, the data and the component itself. | ||
| * @param id: id to use for the output data | ||
| * If a closure, it will be called with the id, the data and the component itself. | ||
| * @param auto: auto options to pass to the components | ||
| * | ||
| * @return: a workflow that runs the components | ||
| **/ | ||
| def runEach(Map args) { | ||
| assert args.components: "runEach should be passed a list of components to run" | ||
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| def components_ = args.components | ||
| if (components_ !instanceof List) { | ||
| components_ = [ components_ ] | ||
| } | ||
| assert components_.size() > 0: "pass at least one component to runEach" | ||
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| def fromState_ = args.fromState | ||
| def toState_ = args.toState | ||
| def filter_ = args.filter | ||
| def id_ = args.id | ||
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| workflow runEachWf { | ||
| take: input_ch | ||
| main: | ||
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| // generate one channel per method | ||
| out_chs = components_.collect{ comp_ -> | ||
| filter_ch = filter_ | ||
| ? input_ch | filter{tup -> | ||
| filter_(tup[0], tup[1], comp_) | ||
| } | ||
| : input_ch | ||
| id_ch = id_ | ||
| ? filter_ch | map{tup -> | ||
| // def new_id = id_(tup[0], tup[1], comp_) | ||
| def new_id = tup[0] | ||
| if (id_ instanceof String) { | ||
| new_id = id_ | ||
| } else if (id_ instanceof Closure) { | ||
| new_id = id_(new_id, tup[1], comp_) | ||
| } | ||
| [new_id] + tup.drop(1) | ||
| } | ||
| : filter_ch | ||
| data_ch = id_ch | map{tup -> | ||
| def new_data = tup[1] | ||
| if (fromState_ instanceof Map) { | ||
| new_data = fromState_.collectEntries{ key0, key1 -> | ||
| [key0, new_data[key1]] | ||
| } | ||
| } else if (fromState_ instanceof List) { | ||
| new_data = fromState_.collectEntries{ key -> | ||
| [key, new_data[key]] | ||
| } | ||
| } else if (fromState_ instanceof Closure) { | ||
| new_data = fromState_(tup[0], new_data, comp_) | ||
| } | ||
| tup.take(1) + [new_data] + tup.drop(1) | ||
| } | ||
| out_ch = data_ch | ||
| | comp_.run( | ||
| auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] | ||
| ) | ||
| post_ch = toState_ | ||
| ? out_ch | map{tup -> | ||
| def output = tup[1] | ||
| def old_state = tup[2] | ||
| if (toState_ instanceof Map) { | ||
| new_state = old_state + toState_.collectEntries{ key0, key1 -> | ||
| [key0, output[key1]] | ||
| } | ||
| } else if (toState_ instanceof List) { | ||
| new_state = old_state + toState_.collectEntries{ key -> | ||
| [key, output[key]] | ||
| } | ||
| } else if (toState_ instanceof Closure) { | ||
| new_state = toState_(tup[0], output, old_state, comp_) | ||
| } | ||
| [tup[0], new_state] + tup.drop(3) | ||
| } | ||
| : out_ch | ||
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| post_ch | ||
| } | ||
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| // mix all results | ||
| output_ch = | ||
| (out_chs.size == 1) | ||
| ? out_chs[0] | ||
| : out_chs[0].mix(*out_chs.drop(1)) | ||
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| emit: output_ch | ||
| } | ||
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| return runEachWf | ||
| } |
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