Fix minor typos in changelogs/source code

README.md

@@ -184,7 +184,7 @@ Community
 You can post questions, or report problems by using the Nextflow [discussions](https://github.com/nextflow-io/nextflow/discussions)
 or the Nextflow [Slack community chat](https://www.nextflow.io/slack-invite.html).
 
-*Nextflow* also hosts a yearly workshop showcasing researcher's workflows and advancements in the langauge. Talks from the past workshops are available on the [Nextflow YouTube Channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)
+*Nextflow* also hosts a yearly workshop showcasing researcher's workflows and advancements in the language. Talks from the past workshops are available on the [Nextflow YouTube Channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)
 
 The [nf-core](https://nf-co.re/) project is a community effort aggregating high quality *Nextflow* workflows which can be used by the community. 
 

build.gradle

@@ -24,7 +24,7 @@ plugins {
 def groovyVer = System.getenv('CI_GROOVY_VERSION')
 if (groovyVer) {
     def repo = groovyVer.startsWith('com.github.apache:') ? 'https://jitpack.io' : 'https://oss.jfrog.org/oss-snapshot-local/'
-    logger.lifecycle "Overriden Groovy dependency to use $groovyVer - repository: $repo"
+    logger.lifecycle "Overridden Groovy dependency to use $groovyVer - repository: $repo"
     allprojects {
         repositories {
             maven { url repo }

changelog.txt

@@ -164,7 +164,7 @@ NEXTFLOW CHANGE-LOG
 - Add Wave containers reports (preview) [9d9e2758]
 - Add disk resource with type option for google batch (#3861) [166b3638]
 - Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
-- Add plugin cmd help descrption [d3788f9f]
+- Add plugin cmd help description [d3788f9f]
 - Add retry policy on Az blob operations [295bc1ff]
 - Add retry policy to Wave http client [1daebeef]
 - Add support for AWS SES as mail sending provider [df85d443]
@@ -188,7 +188,7 @@ NEXTFLOW CHANGE-LOG
 - Improve description of channels and channel types (#4120) [8975734d]
 - Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
 - Minor change in Wave config [4da0442a]
-- Prevent null exit code when Google batch is unable to acces exit status [f68a39ec]
+- Prevent null exit code when Google batch is unable to access exit status [f68a39ec]
 - Refactor Conda and Spack support for Wave to Java [36b9e226]
 - Remove `--no-home` default option from charliecloud builder (#3956) [915074a4]
 - Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
@@ -225,7 +225,7 @@ NEXTFLOW CHANGE-LOG
 - Enable static compilation to missing classes (#3906) [c3c4b2f0]
 - Fix -with-conda option in the docs (#3867) [9b350ba8]
 - Fix AWS SSE env propagation to Fusion [e24608c3]
-- Fix Apptainer rendering by removing superflous space [36607ed1]
+- Fix Apptainer rendering by removing superfluous space [36607ed1]
 - Fix Azure jobs correctly deleted after completion (#3927) [b173a983]
 - Fix Azure pool creation when using scaling formula (#3868) [79984a87]
 - Fix DSL2 support in nextflow console (#3864) [0253f8d7]
@@ -787,7 +787,7 @@ NEXTFLOW CHANGE-LOG
 - Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
 - Fix Default plugins are overridden by config plugins [46cf3bfa] <Paolo Di Tommaso>
 - Fix S3 transfer download directory [b7bf9fe5]
-- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
+- Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] <Jorge Aguilera>
 - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
 - Fix AWS Batch job definition conflict (#3048) [e5084418]
 - Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416d]
@@ -847,7 +847,7 @@ NEXTFLOW CHANGE-LOG
 - Add DirWatcher v2 [209c82cd]
 - Add Moriondo in the list of random names [e0abca58]
 - Add preview CLI option (#2914) [aa8f1aa4]
-- Fix Git config resultion error [64436697]
+- Fix Git config resolution error [64436697]
 - Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] <Jorge Aguilera>
 - Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] <Jorge Aguilera>
 - Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] <Prete>
@@ -862,14 +862,14 @@ NEXTFLOW CHANGE-LOG
 - Add Hyperqueue executor (#2896) [ffa5712e] <Henrik Nortamo>
 - Add support for K8s Job resource [c70eb12d] <xhejtman>
 - Add support for time process directive in GLS executor (#2880) [1402e183] <Florian De Temmerman>
-- Add support for priviledge option for K8s containers [7ffe3a02]
+- Add support for privilege option for K8s containers [7ffe3a02]
 - Add DSL1 option to docs (#2836) [d30841a5] <Jose Espinosa-Carrasco>
 - Add support for container options to Azure Batch [3f4f00f9] 
 - Add support for move operation to AWS S3 [8c0ddfd5] 
 - Add K8s execution hostname in the trace file (#2828) [ebaef92a] <Fabian Lehmann>
-- Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
+- Add support for AWS S3 encryption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
 - Add support for Micromamba [383e023f]
-- Add jaxb-api dependecy to nf-amazon [c1a09f87]
+- Add jaxb-api dependency to nf-amazon [c1a09f87]
 - Add strict mode config setting [696e70b5]
 - Add -head-prescript option to kuberun (#2830) [9e387055] 
 - Fix missing err message on submit failure [233e67f0] (#2899)
@@ -974,7 +974,7 @@ NEXTFLOW CHANGE-LOG
 - Prevent invalid use of large maxForks values [5de0c200]
 - Prevent race condition on thread pool creation [3e707a1d]
 - Refactor AWS batch job unique token generation [d64f5a21]
-- Decrese log verbosity [9237d587] [d1a5e5a8]
+- Decrease log verbosity [9237d587] [d1a5e5a8]
 - Throw an error if a required secret is missing [8e5129d6]
 - Wait for pod to stop running before shutdown (#2667) [505c5ad6]) <kfrancisdev>
 - Restore AZ tests [858a4568]
@@ -985,7 +985,7 @@ NEXTFLOW CHANGE-LOG
 22.02.0-edge - 25 Feb 2022
 - Fix Prevent S3 tagging with empty list [ae7db466]
 - Fix Azure repos tests [856aacf0]
-- Fix isse on includeConfig resolution #2675 [6591a9e1]
+- Fix issue on includeConfig resolution #2675 [6591a9e1]
 - Fix NPE when accessing not existing Git file [6c79f8fd]
 - Fix Batch Job name exceed max allowed size [e8b70ca3]
 - Fix detect and skip bom mark in files (#2645) [02b06ba3] <Jorge Aguilera>
@@ -1145,7 +1145,7 @@ NEXTFLOW CHANGE-LOG
 - Fix verbose logging [92b113134]
 - Fix docker image url [ed24a475d]
 - Fix Temporary directories not deleted in on_exit #2406 [181bdf528] <Lukas Jelonek>
-- Fix implict authentication for resources served by Tower [e30310b4f]
+- Fix implicit authentication for resources served by Tower [e30310b4f]
 - Fix No more of 255 channels can be defined into a workflow context #2417 [7f91ecb39]
 - Add tip about escaping variables in env scope #2366 <Ben Shealy>
 - Add K8s env fieldPath option to pod directive #2363 <Ben Shealy>
@@ -1233,7 +1233,7 @@ NEXTFLOW CHANGE-LOG
 21.06.0-edge - 3 Jul 2021
 - Add Keep alive option to Google LS executor [994222074]
 - Add support for FTP proxy and proxy servers authentication [8ec33b04d]
-- Add support for plugins groupping [aa5bc7d34]
+- Add support for plugins grouping [aa5bc7d34]
 - Add More details about the reason why a AWS Batch job has failed #2146 [27a4e88b2]
 - Add support for extensions priority [ae083f1aa]
 - Add stubRun attribute to workflow metadata #2164 [86cfc66fd]
@@ -1298,7 +1298,7 @@ NEXTFLOW CHANGE-LOG
 - Add readOnly flag to k8s volume mounts (#2013) [33bd24ac]
 - Add Start default plugins on-demand #1964 [cf2a9d73]
 - Add support for tower workspaceId [e2977688]
-- Improve suppor for BitBucket server repos [eb946e27]
+- Improve support for BitBucket server repos [eb946e27]
 - Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985]
 - Fix regression caused by nested params handling #1923 [b25af49b]
 - Fix Cache invalidation when repo is cloned between runs #1989 [ac526f38]
@@ -1444,7 +1444,7 @@ NEXTFLOW CHANGE-LOG
 - Remove unneeded parentheses from stdout declaration [dc029c04]
 - Merge execution logs command docs [577ec744]
 - Passing exact memory to TES executor in GiB #1696 [c8a15545]
-- Improve docs replacing suscribe{println it} with view() [f84ccb6f] [cb2d607d]
+- Improve docs replacing subscribe{println it} with view() [f84ccb6f] [cb2d607d]
 - Use current environment Bash #1598 #1614 [e70ef87a]
 - Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45]
 - Update Bitbucket docs [b9b57f83]
@@ -1884,7 +1884,7 @@ NEXTFLOW CHANGE-LOG
 - Fixed remote bin directory when using bucketDir option [6d796783]
 - Fixed foreign file system detection [1489cc72]
 - Fixed Ansi logger division by zero [ae2b1380]
-- Fixed Unparseable Data format on http file #962
+- Fixed Unparsable Data format on http file #962
 - Fixed Log command history #405
 - Fixed Too long process tag name can cause SLURM failure #941
 - Fixed LSF can return an inconsistent jobs status #927
@@ -1936,7 +1936,7 @@ NEXTFLOW CHANGE-LOG
 - Fixed remote bin directory when using buckerDir option [6d796783]
 - Fixed foreign file system detection [1489cc72]
 - Fixed Ansi logger division by zero [ae2b1380]
-- Fixed Unparseable Data format on http file #962
+- Fixed Unparsable Data format on http file #962
 - Fixed Log command history #405
 - Fixed Too long process tag name can cause SLURM failure #941
 - Fixed LSF can return an inconsistent jobs status #927
@@ -2438,7 +2438,7 @@ NEXTFLOW CHANGE-LOG
 0.23.3 - 9 Feb 2017
 - Fixed Job termination is not recognised if the starter file is not created #268
 - Fixed Allow NF console to resume process executions (second take) #280
-- Fixed PublishDir may throw a FileAlredyExistsException #283
+- Fixed PublishDir may throw a FileAlreadyExistsException #283
 - Increased logger file appender buffer size to 64kb
 - Updated Logback to version 1.1.10
 - Updated copyright info

modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy

@@ -255,7 +255,7 @@ class MermaidRenderer implements DagRenderer {
      * @param nodeLookup
      */
     private Map getNodeTree(Map<DAG.Vertex,Node> nodeLookup) {
-        // infer subgraphs of operator nodess
+        // infer subgraphs of operator nodes
         final inferredKeys = inferSubgraphKeys(nodeLookup)
 
         // construct node tree

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

@@ -373,7 +373,7 @@ class TaskProcessor {
      * Create a "preview" for a task run. This method is only meant for the creation of "mock" task run
      * to allow the access for the associated {@link TaskConfig} during a pipeline "preview" execution.
      *
-     * Note this returns an "eventually" task configuration object. Also Inputs ane output parameters are NOT
+     * Note this returns an "eventually" task configuration object. Also Inputs and output parameters are NOT
      * resolved by this method.
      *
      * @return A {@link TaskRun} object holding a reference to the associated {@link TaskConfig}
@@ -2426,7 +2426,7 @@ class TaskProcessor {
 
         @Override
         List<Object> beforeRun(final DataflowProcessor processor, final List<Object> messages) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> Before run -- messages: ${messages}"
             // the counter must be incremented here, otherwise it won't be consistent
@@ -2443,15 +2443,15 @@ class TaskProcessor {
 
         @Override
         void afterRun(DataflowProcessor processor, List<Object> messages) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> After run"
             currentTask.remove()
         }
 
         @Override
         Object messageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2463,7 +2463,7 @@ class TaskProcessor {
 
         @Override
         Object controlMessageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2473,7 +2473,7 @@ class TaskProcessor {
             super.controlMessageArrived(processor, channel, index, message)
 
             if( message == PoisonPill.instance ) {
-                // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+                // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
                 if( log.isTraceEnabled() )
                     log.trace "<${name}> Poison pill arrived; port: $index"
                 openPorts.set(index, 0) // mark the port as closed
@@ -2485,7 +2485,7 @@ class TaskProcessor {
 
         @Override
         void afterStop(final DataflowProcessor processor) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> After stop"
         }

modules/nextflow/src/main/java/de/javakaffee/kryoserializers/UnmodifiableCollectionsSerializer.java

@@ -78,7 +78,7 @@ public Object read(final Kryo kryo, final Input input, final Class<Object> clazz
     public void write(final Kryo kryo, final Output output, final Object object) {
         try {
             final UnmodifiableCollection unmodifiableCollection = UnmodifiableCollection.valueOfType( object.getClass() );
-            // the ordinal could be replaced by s.th. else (e.g. a explicitely managed "id")
+            // the ordinal could be replaced by s.th. else (e.g. a explicitly managed "id")
             output.writeInt( unmodifiableCollection.ordinal(), true );
             kryo.writeClassAndObject( output, unmodifiableCollection.sourceCollectionField.get( object ) );
         } catch ( final RuntimeException e ) {

plugins/nf-amazon/changelog.txt

@@ -115,7 +115,7 @@ nf-amazon changelog
 
 1.9.0 - 1 Aug 2022
 - Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
-- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
+- Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] <Jorge Aguilera>
 - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b] <Paolo Di Tommaso>
 - Fix AWS Batch job definition conflict (#3048) [e5084418] <Paolo Di Tommaso>
 - Improve S3 file upload/download via Transfer manager [7e8d2a5a] [b7bf9fe5] <Jorge Aguilera>

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java

@@ -226,7 +226,7 @@ public void copyObject(CopyObjectRequest req, List<Tag> tags, String contentType
 		if( cannedAcl != null ) {
 			req.withCannedAccessControlList(cannedAcl);
 		}
-		// getNewObjectMetada returns null if no object metadata has been specified.
+		// getNewObjectMetadata returns null if no object metadata has been specified.
 		ObjectMetadata meta = req.getNewObjectMetadata() != null ? req.getNewObjectMetadata() : new ObjectMetadata();
 		if( storageEncryption != null ) {
 			meta.setSSEAlgorithm(storageEncryption.toString());

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

@@ -29,7 +29,7 @@
 
 /**
  * S3 iterator over folders at first level.
- * Future verions of this class should be return the elements
+ * Future versions of this class should be return the elements
  * in a incremental way when the #next() method is called.
  */
 public class S3Iterator implements Iterator<Path> {

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java

@@ -235,7 +235,7 @@ private MessageDigest createMd5() {
 
     /**
      * Writes a byte into the uploader buffer. When it is full starts the upload process
-     * in a asynchornous manner
+     * in a asynchronous manner
      *
      * @param b The byte to be written
      * @throws IOException
@@ -384,7 +384,7 @@ public void run() {
     }
 
     /**
-     * Close the stream uploading any remaning buffered data
+     * Close the stream uploading any remaining buffered data
      *
      * @throws IOException
      */

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3CopyStream.java

@@ -150,7 +150,7 @@ public void write(byte b[], int off, int len) throws IOException {
 
     /**
      * Writes a byte into the uploader buffer. When it is full starts the upload process
-     * in a asynchornous manner
+     * in a asynchronous manner
      *
      * @param b The byte to be written
      * @throws IOException
@@ -166,7 +166,7 @@ public void write (int b) throws IOException {
 
 
     /**
-     * Close the stream uploading any remaning buffered data
+     * Close the stream uploading any remaining buffered data
      *
      * @throws IOException
      */

plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiCallback.java

@@ -66,10 +66,10 @@ public interface ApiCallback<T> {
     void onUploadProgress(long bytesWritten, long contentLength, boolean done);
 
     /**
-     * This is called when the API downlond processing.
+     * This is called when the API download processing.
      *
      * @param bytesRead bytes Read
-     * @param contentLength content lenngth of the response
+     * @param contentLength content length of the response
      * @param done Read end
      */
     void onDownloadProgress(long bytesRead, long contentLength, boolean done);

plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiClient.java

@@ -606,7 +606,7 @@ public ApiClient setDebugging(boolean debugging) {
     /**
      * The path of temporary folder used to store downloaded files from endpoints
      * with file response. The default value is <code>null</code>, i.e. using
-     * the system's default tempopary folder.
+     * the system's default temporary folder.
      *
      * @see <a href="https://docs.oracle.com/javase/7/docs/api/java/io/File.html#createTempFile">createTempFile</a>
      * @return Temporary folder path
@@ -616,7 +616,7 @@ public String getTempFolderPath() {
     }
 
     /**
-     * Set the tempoaray folder path (for downloading files)
+     * Set the temporary folder path (for downloading files)
      *
      * @param tempFolderPath Temporary folder path
      * @return ApiClient
@@ -1195,7 +1195,7 @@ public String buildUrl(String path, List<Pair> queryParams) {
      * Set header parameters to the request builder, including default headers.
      *
      * @param headerParams Header parameters in the ofrm of Map
-     * @param reqBuilder Reqeust.Builder
+     * @param reqBuilder Request.Builder
      */
     public void processHeaderParams(Map<String, String> headerParams, Request.Builder reqBuilder) {
         for (Entry<String, String> param : headerParams.entrySet()) {

plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/model/TesExecutor.java

@@ -197,10 +197,10 @@ public TesExecutor putEnvItem(String key, String envItem) {
   }
 
    /**
-   * Enviromental variables to set within the container.
+   * Environmental variables to set within the container.
    * @return env
   **/
-  @ApiModelProperty(value = "Enviromental variables to set within the container.")
+  @ApiModelProperty(value = "Environmental variables to set within the container.")
   public Map<String, String> getEnv() {
     return env;
   }

tests/rnaseq-toy-dsl2.nf

@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 /*
- * Defines pipeline parameters in order to specify the refence genomes
+ * Defines pipeline parameters in order to specify the reference genomes
  * and read pairs by using the command line options
  */
 params.reads = "$baseDir/data/ggal/*_{1,2}.fq"