myFile.withReader { ... } Found a problem. A BUG ?

[wan230114]

Bug report

program:

// BUG 
myFile = file('./my_file.txt')
myFile.text = 'Hello world!\n'  // 文件覆写
myFile.append('Add this line\n')  // 文件追加
myFile << 'Add a line more\n'  // 文件追加

println '\n---\nfile1：'
print myFile.text

println '\n---\ntest1：'
myFile.withReader {
    String line_tmp2
    while ( line_tmp2 = it.readLine() ) {
        println line_tmp2
    }
}

// normal
myFile = file('./my_file.txt')
myFile.text = 'Hello world!\n\n'  // 文件覆写
myFile.append('Add this line\n')  // 文件追加
myFile << 'Add a line more\n'  // 文件追加

println '\n---\nfile2：'
print myFile.text

println '\n---\ntest2：'
myFile.withReader {
    String line_tmp2
    while ( line_tmp2 = it.readLine() ) {
        println line_tmp2
    }
}

Expected behavior and actual behavior

(Give an brief description of the expected behavior
and actual behavior)

Output of this program:

---
file1：
Hello world!
Add this line
Add a line more


---
test1：
Hello world!
Add this line
Add a line more

---
file2：
Hello world!

Add this line
Add a line more


---
test2：
Hello world!

The correct output should be:

---
file1：
Hello world!
Add this line
Add a line more


---
test1：
Hello world!
Add this line
Add a line more

---
file2：
Hello world!

Add this line
Add a line more


---
test2：
Hello world!

Add this line
Add a line more

Program output

log file.

.nextflow.log:

Oct-08 04:04:43.054 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /work/work_users/chenjun/pipeline/Notes/how-to-run/nextflow/tutorial-bug.nf
Oct-08 04:04:43.269 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.04.0
Oct-08 04:04:43.316 [main] INFO  nextflow.cli.CmdRun - Launching `/work/work_users/chenjun/pipeline/Notes/how-to-run/nextflow/tutorial-bug.nf` [backstabbing_knuth] - revision: 23eca9db8b
Oct-08 04:04:43.469 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/chenjun/.nextflow/plugins
Oct-08 04:04:43.473 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-08 04:04:43.478 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
Oct-08 04:04:43.493 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-08 04:04:43.495 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-08 04:04:43.505 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-08 04:04:43.532 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct-08 04:04:43.687 [main] DEBUG nextflow.Session - Session uuid: 70ab4112-ca4f-4de5-b46f-aff26643e6b4
Oct-08 04:04:43.687 [main] DEBUG nextflow.Session - Run name: backstabbing_knuth
Oct-08 04:04:43.691 [main] DEBUG nextflow.Session - Executor pool size: 4
Oct-08 04:04:43.718 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 21.04.0 build 5552
  Created: 02-05-2021 16:22 UTC (03-05-2021 00:22 CDT)
  System: Linux 3.10.0-957.el7.x86_64
  Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12
  Encoding: UTF-8 (UTF-8)
  Process: [email protected] [192.168.241.135]
  CPUs: 4 - Mem: 11.9 GB (1.7 GB) - Swap: 2 GB (1.9 GB)
Oct-08 04:04:43.765 [main] DEBUG nextflow.Session - Work-dir: /work/work_users/chenjun/pipeline/Notes/how-to-run/nextflow/work [ext2/ext3]
Oct-08 04:04:43.766 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /work/work_users/chenjun/pipeline/Notes/how-to-run/nextflow/bin
Oct-08 04:04:43.792 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-08 04:04:43.816 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-08 04:04:44.208 [main] DEBUG nextflow.Session - Session start invoked
Oct-08 04:04:45.717 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-08 04:04:45.774 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: 
Oct-08 04:04:45.825 [main] INFO  nextflow.script.BaseScript - 
---
file1：
Oct-08 04:04:45.828 [main] INFO  nextflow.script.BaseScript - Hello world!
Add this line
Add a line more

Oct-08 04:04:45.828 [main] INFO  nextflow.script.BaseScript - 
---
test1：
Oct-08 04:04:45.842 [main] INFO  nextflow.script.BaseScript - Hello world!
Oct-08 04:04:45.843 [main] INFO  nextflow.script.BaseScript - Add this line
Oct-08 04:04:45.843 [main] INFO  nextflow.script.BaseScript - Add a line more
Oct-08 04:04:45.848 [main] INFO  nextflow.script.BaseScript - 
---
file2：
Oct-08 04:04:45.849 [main] INFO  nextflow.script.BaseScript - Hello world!

Add this line
Add a line more

Oct-08 04:04:45.850 [main] INFO  nextflow.script.BaseScript - 
---
test2：
Oct-08 04:04:45.853 [main] INFO  nextflow.script.BaseScript - Hello world!
Oct-08 04:04:45.857 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Oct-08 04:04:45.858 [main] DEBUG nextflow.Session - Session await
Oct-08 04:04:45.858 [main] DEBUG nextflow.Session - Session await > all process finished
Oct-08 04:04:45.858 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-08 04:04:45.887 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Oct-08 04:04:46.117 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Oct-08 04:04:46.240 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Environment

• Nextflow version: version 21.04.0 build 5552
• Java version: 1.8.0_152-release
• Operating system: CentOS Linux release 7.6.1810 (Core)
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)