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rpetit3rpetit3
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tweaks for new structure
1 parent d0e3994 commit 2230caa

19 files changed

+62
-62
lines changed

‎build.gradle‎

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@@ -2,15 +2,15 @@ plugins {
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id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha4'
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}
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version = '0.1.0'
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dependencies {
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// add here plugins dependencies
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implementation 'org.json:json:20240303'
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implementation 'dev.harrel:json-schema:1.5.0'
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implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
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}
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version = '0.1.0'
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nextflowPlugin {
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nextflowVersion = '24.10.0'
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‎settings.gradle‎

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@@ -1 +1 @@
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rootProject.name = 'bactopia'
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rootProject.name = 'nf-bactopia'

‎src/main/groovy/bactopia/plugin/BactopiaConfig.groovy‎

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@@ -1,4 +1,4 @@
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.util.logging.Slf4j
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‎src/main/groovy/bactopia/plugin/BactopiaExtension.groovy‎

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@@ -14,7 +14,7 @@
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.json.JsonBuilder
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import org.json.JSONObject
@@ -29,15 +29,15 @@ import nextflow.plugin.extension.PluginExtensionPoint
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import nextflow.script.WorkflowMetadata
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import nextflow.Session
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import nextflow.bactopia.BactopiaConfig
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import nextflow.bactopia.BactopiaSchema
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import nextflow.bactopia.nfschema.SummaryCreator
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import bactopia.plugin.BactopiaConfig
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import bactopia.plugin.BactopiaSchema
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import bactopia.plugin.nfschema.SummaryCreator
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import static nextflow.bactopia.inputs.BactopiaTools.collectInputs
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import static nextflow.bactopia.BactopiaTemplate.getLogColors
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import static nextflow.bactopia.BactopiaTemplate.getLogo
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import static nextflow.bactopia.BactopiaTemplate.getWorkflowSummary
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import static nextflow.bactopia.nfschema.Common.getLongestKeyLength
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import static bactopia.plugin.inputs.BactopiaTools.collectInputs
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import static bactopia.plugin.BactopiaTemplate.getLogColors
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import static bactopia.plugin.BactopiaTemplate.getLogo
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import static bactopia.plugin.BactopiaTemplate.getWorkflowSummary
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import static bactopia.plugin.nfschema.Common.getLongestKeyLength
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/**
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* Example plugin extension showing how to implement a basic

‎src/main/groovy/bactopia/plugin/BactopiaFactory.groovy‎

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@@ -14,7 +14,7 @@
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.transform.CompileStatic
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import nextflow.Session

‎src/main/groovy/bactopia/plugin/BactopiaMotD.groovy‎

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@@ -1,8 +1,8 @@
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.util.logging.Slf4j
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import static nextflow.bactopia.BactopiaTemplate.getLogColors
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import static bactopia.plugin.BactopiaTemplate.getLogColors
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@Slf4j
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class BactopiaMotD {

‎src/main/groovy/bactopia/plugin/BactopiaObserver.groovy‎

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@@ -14,7 +14,7 @@
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.transform.CompileStatic
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import groovy.util.logging.Slf4j
@@ -23,9 +23,9 @@ import java.nio.file.Paths
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import nextflow.Session
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import nextflow.trace.TraceObserver
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import nextflow.bactopia.BactopiaConfig
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import nextflow.bactopia.nfschema.HelpMessageCreator
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import static nextflow.bactopia.BactopiaMotD.getMotD
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import bactopia.plugin.BactopiaConfig
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import bactopia.plugin.nfschema.HelpMessageCreator
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import static bactopia.plugin.BactopiaMotD.getMotD
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/**
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* Bactopia workflow observer

‎src/main/groovy/bactopia/plugin/BactopiaPlugin.groovy‎

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@@ -14,7 +14,7 @@
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.transform.CompileStatic
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import nextflow.plugin.BasePlugin

‎src/main/groovy/bactopia/plugin/BactopiaSchema.groovy‎

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//
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// This is based on the original NF-Core template (the OG 'libs' folder) and the nf-validation
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// plugin (which you should probably be using instead of this file).
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.json.JsonBuilder
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import groovy.json.JsonSlurper
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import nextflow.util.Duration
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import nextflow.util.MemoryUnit
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import nextflow.bactopia.BactopiaConfig
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import nextflow.bactopia.nfschema.JsonSchemaValidator
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import bactopia.plugin.BactopiaConfig
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import bactopia.plugin.nfschema.JsonSchemaValidator
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import static nextflow.bactopia.nfschema.Common.getBasePath
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import static nextflow.bactopia.BactopiaUtils.isLocal
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import static nextflow.bactopia.BactopiaUtils.isPositiveInteger
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import static nextflow.bactopia.BactopiaUtils.fileNotFound
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import static nextflow.bactopia.BactopiaUtils.fileNotGzipped
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import static nextflow.bactopia.BactopiaTemplate.getLogColors
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import static nextflow.bactopia.BactopiaTemplate.logError
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import static bactopia.plugin.nfschema.Common.getBasePath
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import static bactopia.plugin.BactopiaUtils.isLocal
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import static bactopia.plugin.BactopiaUtils.isPositiveInteger
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import static bactopia.plugin.BactopiaUtils.fileNotFound
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import static bactopia.plugin.BactopiaUtils.fileNotGzipped
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import static bactopia.plugin.BactopiaTemplate.getLogColors
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import static bactopia.plugin.BactopiaTemplate.logError
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@Slf4j
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class BactopiaSchema {

‎src/main/groovy/bactopia/plugin/BactopiaTemplate.groovy‎

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//
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// This is based on the original NF-Core template (the OG 'libs' folder) and the nf-validation
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// plugin (which you should probably be using instead of this file).
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package nextflow.bactopia
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package bactopia.plugin
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import groovy.util.logging.Slf4j
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