add codespell: config, workflow and have typos fixed

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,timeline-expected.html,*.fq,*.min.js,ScriptDslTest.groovy
+# some cases where we need to catch using regex
+ignore-regex = \bhel\*|fo\\
+# some variables, names, etc to ignore
+ignore-words-list = splitted,ois,tre,marge,smoot,afile,bams,bais

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

changelog.txt

@@ -1307,7 +1307,7 @@ NEXTFLOW CHANGE-LOG
 - Fix az path handling curly brackets globs #1969 [c78a1bbf]
 - Fix Missing git credentials when checking last commit id [f101308e]
 - Fix plugins version check against local installation [535c2bb5]
-- Fix local dependant formatting #1962 [2a5cbac1]
+- Fix local dependent formatting #1962 [2a5cbac1]
 - Fix Encode path parameter at GitLab getContentUrl [6f80f651]
 - Fix Only use sudo rm with docker #1956 [f9490423]
 - Prevent AZ NPE when missing vmtype + better logging #1992 [711362ca]
@@ -1375,7 +1375,7 @@ NEXTFLOW CHANGE-LOG
 - Add support for basic auth for http/s file provider [6027fcba]
 - Add User-Agent info to httpfs requests [222637de]
 - Update CPU and RAM for containers (#1833) [ccf5c8ba]
-- Move test containes to quay.io [7db053eb] [773be707] [c10a7f53]
+- Move test contains to quay.io [7db053eb] [773be707] [c10a7f53]
 
 20.12.0-edge - 12 Dec 2020 
 - Add support for charliecloud container engine #1809
@@ -1749,7 +1749,7 @@ NEXTFLOW CHANGE-LOG
 - Add Pbs Pro execution documentation [1d39ab31]
 - Add code of conduct document
 - Fix missing LFS executor register invocation #1234 [b1b7ab1]
-- Fix "invalid pod status" when running scrips with the kubernetes executor #1242 [11caac68]
+- Fix "invalid pod status" when running scripts with the kubernetes executor #1242 [11caac68]
 - Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8]
 - (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`)
 

docs/conf.py

@@ -299,7 +299,7 @@
 # The format is a list of tuples containing the path and title.
 #epub_pre_files = []
 
-# HTML files shat should be inserted after the pages created by sphinx.
+# HTML files that should be inserted after the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
 #epub_post_files = []
 

docs/sharing.md

@@ -110,7 +110,7 @@ The `pull` command allows you to download a project from a GitHub repository or
 nextflow pull nextflow-io/examples
 ```
 
-Altenatively, you can use the repository URL as the name of the project to pull:
+Alternatively, you can use the repository URL as the name of the project to pull:
 
 ```bash
 nextflow pull https://github.com/nextflow-io/examples

modules/nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy

@@ -71,7 +71,7 @@ class ASTHelpers {
 
     /**
      * Creates a new {@code ConstructorCallExpression} for the specified class and arguments
-     * specified using an open array. Te
+     * specified using an open array.
      *
      * @param clazz The {@code Class} for which the create a constructor call expression
      * @param args The arguments to be passed to the constructor, they will be wrapped by in a {@code ArgumentListExpression}

modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy

@@ -1218,7 +1218,7 @@ class NextflowDSLImpl implements ASTTransformation {
          * @return A tuple in which:
          *      <li>1st item: {@code true} if successful or {@code false} otherwise
          *      <li>2nd item: on error condition the line containing the error in the source script, zero otherwise
-         *      <li>3nd item: on error condition the column containing the error in the source script, zero otherwise
+         *      <li>3rd item: on error condition the column containing the error in the source script, zero otherwise
          *
          */
         protected boolean wrapExpressionWithClosure( BlockStatement block, Expression expr, int len, CharSequence source, SourceUnit unit ) {

modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy

@@ -60,6 +60,6 @@ class CmdDrop extends CmdBase {
             return
         }
 
-        throw new AbortOperationException("Local project repository contains uncommitted changes -- wont drop it")
+        throw new AbortOperationException("Local project repository contains uncommitted changes -- won't drop it")
     }
 }

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -321,7 +321,7 @@ class ConfigBuilder {
     }
 
     protected Map configVars() {
-        // this is needed to make sure to re-use the same
+        // this is needed to make sure to reuse the same
         // instance of the config vars across different instances of the ConfigBuilder
         // and prevent multiple parsing of the same params file (which can even be remote resource)
         return cacheableConfigVars(baseDir)

modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy

@@ -668,7 +668,7 @@ class TaskProcessor {
 
     /**
      * @return A string 'she-bang' formatted to the added on top script to be executed.
-     * The interpreter to be used define bu the *taskConfig* property {@code shell}
+     * The interpreter to be used define by the *taskConfig* property {@code shell}
      */
     static String shebangLine(shell) {
         assert shell, "Missing 'shell' property in process configuration"

modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy

@@ -466,7 +466,7 @@ class TaskRun implements Cloneable {
     /**
      * Get the map of *input* objects by the given {@code InParam} type
      *
-     * @param types One ore more subclass of {@code InParam}
+     * @param types One or more subclass of {@code InParam}
      * @return An associative array containing all the objects for the specified type
      */
     def <T extends InParam> Map<T,Object> getInputsByType( Class<T>... types ) {
@@ -482,7 +482,7 @@ class TaskRun implements Cloneable {
     /**
      * Get the map of *output* objects by the given {@code InParam} type
      *
-     * @param types One ore more subclass of {@code InParam}
+     * @param types One or more subclass of {@code InParam}
      * @return An associative array containing all the objects for the specified type
      */
     def <T extends OutParam> Map<T,Object> getOutputsByType( Class<T>... types ) {

modules/nextflow/src/main/groovy/nextflow/script/IterableDef.groovy

@@ -52,7 +52,7 @@ trait IterableDef {
      * To support component recursion, the feedback channels must be used as the channel instances
      * for the outputs instead of creating new ones
      * 
-     * @return A list of output channels brining the process feedback
+     * @return A list of output channels bringing the process feedback
      */
     List<DataflowWriteChannel> getFeedbackChannels() { outputChannels }
 

modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy

@@ -45,7 +45,7 @@ class WorkflowDef extends BindableDef implements ChainableDef, IterableDef, Exec
 
     private BaseScript owner
 
-    // -- following attributes are mutable and instance dependant
+    // -- following attributes are mutable and instance dependent
     // -- therefore should not be cloned
 
     private ChannelOut output

modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy

@@ -39,7 +39,7 @@ class WorkflowNotifier {
     private Map config
 
     /**
-    * A map representing the variables defined in the script golab scope
+    * A map representing the variables defined in the script global scope
      */
     private Map variables
 

modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy

@@ -176,7 +176,7 @@ class TraceRecord implements Serializable {
     }
 
     /**
-     * Coverts the value to a duration string.
+     * Converts the value to a duration string.
      *
      * See {@link Duration}
      * @param value

modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy

@@ -84,7 +84,7 @@ class ConfigHelper {
     }
 
     /**
-     * Given a list of paths looks for the files ending withe the extension '.jar' and return
+     * Given a list of paths looks for the files ending with the extension '.jar' and return
      * a list containing the original directories, plus the JARs paths
      *
      * @param dirs

modules/nextflow/src/main/resources/nextflow/trace/assets/d3-timeline.js

@@ -177,7 +177,7 @@
       setWidth();
 
       // check if the user wants relative time
-      // if so, substract the first timestamp from each subsequent timestamps
+      // if so, subtract the first timestamp from each subsequent timestamps
       if(timeIsRelative){
         g.each(function (d, i) {
           d.forEach(function (datum, index) {

modules/nextflow/src/test/groovy/nextflow/cli/CmdSecretTest.groovy

@@ -60,7 +60,7 @@ class CmdSecretTest extends Specification {
         tempDir?.deleteDir()
     }
 
-    def 'should validate #COMMAND doesnt accept #ARGUMENTS' () {
+    def 'should validate #COMMAND does not accept #ARGUMENTS' () {
         when:
         new CmdSecret(args: [COMMAND] + ARGUMENTS).run()
 

modules/nextflow/src/testFixtures/groovy/test/BaseSpec.groovy

@@ -21,7 +21,7 @@ import spock.lang.Specification
 import groovy.util.logging.Slf4j
 
 /**
- * Base specification class - It wraps each test into begin-close "test name" strigs
+ * Base specification class - It wraps each test into begin-close "test name" strings
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */

modules/nf-commons/src/main/nextflow/file/FileHelper.groovy

@@ -533,7 +533,7 @@ class FileHelper {
             return true
         }
         catch( IOException e ) {
-            log.trace "Cant read file attributes: $self -- Cause: [${e.class.simpleName}] ${e.message}"
+            log.trace "Can't read file attributes: $self -- Cause: [${e.class.simpleName}] ${e.message}"
             return false
         }
 

modules/nf-commons/src/main/nextflow/file/TagAwareFile.groovy

@@ -18,7 +18,7 @@
 package nextflow.file
 
 /**
- * Defines the interface for annotate a file with one ore more tags
+ * Defines the interface for annotate a file with one or more tags
  * 
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java

@@ -403,7 +403,7 @@ public void close() throws IOException {
                 if (Files.exists(tempFile)) {
                     ObjectMetadata metadata = new ObjectMetadata();
                     metadata.setContentLength(Files.size(tempFile));
-                    // FIXME: #20 ServiceLoader cant load com.upplication.s3fs.util.FileTypeDetector when this library is used inside a ear :(
+                    // FIXME: #20 ServiceLoader can't load com.upplication.s3fs.util.FileTypeDetector when this library is used inside a ear :(
 					metadata.setContentType(Files.probeContentType(tempFile));
 
                     try (InputStream stream = Files.newInputStream(tempFile)) {
@@ -905,7 +905,7 @@ private boolean exists(S3Path path) {
 
 	/**
 	 * Get the Control List, if the path not exists
-     * (because the path is a directory and this key isnt created at amazon s3)
+     * (because the path is a directory and this key isn't created at amazon s3)
      * then return the ACL of the first child.
      *
 	 * @param path {@link S3Path}

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java

@@ -122,7 +122,7 @@ private void parseObjectListing(List<S3Path> listPath, ObjectListing current) {
 
     /**
      * The current #buildRequest() get all subdirectories and her content.
-     * This method filter the keyChild and check if is a inmediate
+     * This method filter the keyChild and check if is a immediate
      * descendant of the keyParent parameter
      * @param keyParent String
      * @param keyChild String

tests/Dockerfile

@@ -5,7 +5,7 @@ MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
 RUN apt-get update -y && apt-get install -q -y gnuplot python && apt-get clean 
 
 #
-# Required PERL moduls
+# Required PERL modules
 #
 RUN cpanm Math::CDF Math::Round && \
   rm -rf /root/.cpanm/work/

tests/bin/AMPA.pl

@@ -322,7 +322,7 @@ sub gnuplot_sld {
     print GP "set grid\n";
     print GP "set data style lines\n";
 
-        # if an outpout has been specified output to it 
+        # if an output has been specified output to it 
     if( $graph_file ne "" ) { 
         print GP "set terminal png large enhanced  size 800 600\n";
         print GP "set output '$graph_file' \n";