Remove mini from Flux submit command (#5229) [ci fast]

Signed-off-by: Phil Ewels <[email protected]>
Co-authored-by: Christopher Hakkaart <[email protected]>

docs/executor.md

@@ -95,7 +95,7 @@ Resource requests and other job characteristics can be controlled via the follow
 
 The `flux` executor allows you to run your pipeline script using the [Flux Framework](https://flux-framework.org).
 
-Nextflow manages each process as a separate job that is submitted to the cluster by using the `flux mini submit` command.
+Nextflow submits each process to the cluster as a separate job using the `flux submit` command.
 
 To enable the Flux executor, set `process.executor = 'flux'` in the `nextflow.config` file.
 

docs/flux.md

@@ -100,7 +100,7 @@ Here is an example of submitting a job and getting the log for it.
 First submit the job:
 
 ```console
-$ flux mini submit echo "HELLO MOTO"
+$ flux submit echo "HELLO MOTO"
 ƒEzWqspb
 ```
 
@@ -114,7 +114,7 @@ HELLO MOTO
 Try submitting a longer job:
 
 ```console
-$ flux mini submit sleep 60
+$ flux submit sleep 60
 ```
 
 And then seeing it in the jobs listing.

modules/nextflow/src/main/groovy/nextflow/executor/FluxExecutor.groovy

@@ -61,7 +61,7 @@ class FluxExecutor extends AbstractGridExecutor {
     @Override
     List<String> getSubmitCommandLine(TaskRun task, Path scriptFile ) {
 
-        List<String> result = ['flux', 'mini', 'submit']
+        List<String> result = ['flux', 'submit']
         result << '--setattr=cwd=' + quote(task.workDir)
         result << '--job-name="' + getJobNameFor(task) + '"'
 

modules/nextflow/src/test/groovy/nextflow/executor/FluxExecutorTest.groovy

@@ -72,27 +72,27 @@ class FluxExecutorTest extends Specification {
         then:
         // Flux doesn't have script headers
         executor.getHeaders(task) == ''
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--queue=delta', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--queue=delta', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1m'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=01', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=01', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1h'
         task.config.clusterOptions = '--tasks-per-node=4'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1h'
         task.config.clusterOptions = '--tasks-per-node=4 --cpus-per-node=4'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '--cpus-per-node=4', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '--cpus-per-node=4', '/bin/bash', 'job.sh']
 
     }
 
@@ -111,9 +111,9 @@ class FluxExecutorTest extends Specification {
         task.name = 'my task'
         task.workDir = Paths.get('/work/path')
         task.config = new TaskConfig()
-        
+
         expect:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '/bin/bash', 'job.sh']
 
     }
 
@@ -135,7 +135,7 @@ class FluxExecutorTest extends Specification {
         task.index = 21
         task.config = new TaskConfig()
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd="/work/some\\ data/path"', '--job-name="nf-my_task"', '--output="/work/some\\ data/path/.command.log"', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd="/work/some\\ data/path"', '--job-name="nf-my_task"', '--output="/work/some\\ data/path/.command.log"', '/bin/bash', 'job.sh']
 
     }
 
@@ -160,8 +160,8 @@ class FluxExecutorTest extends Specification {
         result['ƒ6upwy2MY3'] == AbstractGridExecutor.QueueStatus.RUNNING
         result['ƒ6upcbFjvf'] == AbstractGridExecutor.QueueStatus.HOLD
         result['ƒ6uon2RGVV'] == AbstractGridExecutor.QueueStatus.PENDING
-        result['ƒ6upwy2MY4'] == AbstractGridExecutor.QueueStatus.DONE 
-        result['ƒ6upcbFjvh'] == AbstractGridExecutor.QueueStatus.DONE 
+        result['ƒ6upwy2MY4'] == AbstractGridExecutor.QueueStatus.DONE
+        result['ƒ6upcbFjvh'] == AbstractGridExecutor.QueueStatus.DONE
     }
 
     def testQueueStatusCommand() {