Merge pull request #463 from nextflow-io/update-nxf-ver

Update Nextflow version to latest stable (24.10.0)

.devcontainer/Dockerfile

@@ -0,0 +1,4 @@
+FROM ghcr.io/nextflow-io/training:latest
+
+ENV NXF_VER=24.10.0
+ENV NXF_EDGE=0

.devcontainer/devcontainer.json

@@ -1,6 +1,9 @@
 {
     "name": "nfcore",
-    "image": "ghcr.io/nextflow-io/training:latest",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+    },
     "remoteUser": "gitpod",
     "features": {
         "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}

docs/hello_nextflow/02_hello_world.md

@@ -159,7 +159,7 @@ nextflow run hello-world.nf
 You console output should look something like this:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [reverent_carson] DSL2 - revision: 463b611a35
 
@@ -307,7 +307,7 @@ nextflow run hello-world.nf
 The log output should be very similar to the first time your ran the workflow:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [cranky_sinoussi] DSL2 - revision: 30b437bb96
 
@@ -369,7 +369,7 @@ nextflow run hello-world.nf
 The log output should start looking very familiar:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [mighty_lovelace] DSL2 - revision: 6654bc1327
 
@@ -412,7 +412,7 @@ nextflow run hello-world.nf -resume
 The console output should look similar.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [thirsty_gautier] DSL2 - revision: 6654bc1327
 
@@ -557,7 +557,7 @@ nextflow run hello-world.nf
 If you made all four edits correctly, you should get another successful execution:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [prickly_avogadro] DSL2 - revision: b58b6ab94b
 
@@ -613,7 +613,7 @@ nextflow run hello-world.nf --greeting 'Bonjour le monde!'
 Running this should feel extremely familiar by now.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [cheesy_engelbart] DSL2 - revision: b58b6ab94b
 
@@ -652,7 +652,7 @@ nextflow run hello-world.nf
 The output should look the same.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [wise_waddington] DSL2 - revision: 988fc779cf
 
@@ -671,7 +671,7 @@ nextflow run hello-world.nf --greeting 'Konnichiwa!'
 Nextflow's not complaining, that's a good sign:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [prickly_miescher] DSL2 - revision: 988fc779cf
 
@@ -806,7 +806,7 @@ nextflow run hello-world.nf --greeting 'Hello World!'
 Oh, how exciting! There is now an extra line in the log output, which corresponds to the new process we just added:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [magical_brenner] DSL2 - revision: 0e18f34798
 
@@ -876,7 +876,7 @@ nextflow run hello-world.nf
 Well, it certainly seems to run just fine.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [lonely_pare] DSL2 - revision: b9f1d96905
 
@@ -988,7 +988,7 @@ nextflow run hello-world.nf
 Reverting back to the summary view, the output looks like this again:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [jovial_mccarthy] DSL2 - revision: 53f20aeb70
 
@@ -1159,7 +1159,7 @@ nextflow run hello-world.nf
 Once again we see each process get executed three times:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-world.nf` [angry_spence] DSL2 - revision: d171cc0193
 

docs/hello_nextflow/04_hello_genomics.md

@@ -256,7 +256,7 @@ nextflow run hello-genomics.nf
 The command should produce something like this:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-genomics.nf` [reverent_sinoussi] DSL2 - revision: 41d43ad7fe
 
@@ -406,7 +406,7 @@ nextflow run hello-genomics.nf -resume
 Now if we look at the console output, we see the two processes listed:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-genomics.nf` [grave_volta] DSL2 - revision: 4790abc96a
 
@@ -495,7 +495,7 @@ Funny thing: this _might work_, OR it _might fail_.
 If your workflow run succeeded, run it again until you get an error like this:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-genomics.nf` [loving_pasteur] DSL2 - revision: d2a8e63076
 
@@ -676,7 +676,7 @@ nextflow run hello-genomics.nf
 This time (and every time) everything should run correctly:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-genomics.nf` [special_goldstine] DSL2 - revision: 4cbbf6ea3e
 
@@ -794,7 +794,7 @@ nextflow run hello-genomics.nf -resume
 This should produce the same result as before, right?
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-genomics.nf` [sick_albattani] DSL2 - revision: 46d84642f6
 

docs/hello_nextflow/05_hello_operators.md

@@ -301,7 +301,7 @@ nextflow run hello-operators.nf
 And the output is... all red! Oh no.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-operators.nf` [nice_gates] DSL2 - revision: 43c7de9890
 
@@ -354,7 +354,7 @@ nextflow run hello-operators.nf -resume
 Ah, this time it works.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-operators.nf` [elated_carlsson] DSL2 - revision: 6a5786a6fa
 
@@ -502,7 +502,7 @@ nextflow run hello-operators.nf -resume
 It run fairly quickly, since we're running with `-resume`, but...
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-operators.nf` [mad_edison] DSL2 - revision: 6aea0cfded
 
@@ -627,7 +627,7 @@ nextflow run hello-operators.nf -resume
 Aha! It seems to be working now.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-operators.nf` [special_noyce] DSL2 - revision: 11f7a51bbe
 
@@ -824,7 +824,7 @@ nextflow run hello-operators.nf -resume
 And it works!
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-operators.nf` [modest_gilbert] DSL2 - revision: 4f49922223
 

docs/hello_nextflow/06_hello_config.md

@@ -93,7 +93,7 @@ This should run successfully:
 ```console title="Output"
 Nextflow 24.09.2-edge is available - Please consider updating your version to it
 
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [tender_brahmagupta] DSL2 - revision: 848ff2f9b5
 
@@ -152,7 +152,7 @@ nextflow run main.nf
 As expected, the run fails with an error message that looks like this:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `hello-config/main.nf` [silly_ramanujan] DSL2 - revision: 9129bc4618
 
@@ -310,7 +310,7 @@ nextflow run main.nf
 This will take a bit longer than usual the first time, and you might see the console output stay 'stuck' at this stage for a minute or so:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [extravagant_thompson] DSL2 - revision: 848ff2f9b5
 
@@ -325,7 +325,7 @@ That's because Nextflow has to retrieve the Conda packages and create the enviro
 After a few moments, it should spit out some more output, and eventually complete without error.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [silly_goldstine] DSL2 - revision: a60f9fd6af
 
@@ -402,7 +402,7 @@ nextflow run main.nf -profile conda_on
 It works! Convenient, isn't it?
 
 ```
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [sharp_gauss] DSL2 - revision: 66cd7c255a
 
@@ -478,7 +478,7 @@ As expected, this fails with a fairly unambiguous error:
 
 ```console title="Output"
 nextflow
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [grave_gauss] DSL2 - revision: 66cd7c255a
 
@@ -581,7 +581,7 @@ nextflow run main.nf -profile docker_on,local_exec
 With that, we've returned to the original configuration of using Docker containers with local execution, not that you can tell from the console output:
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [irreverent_bassi] DSL2 - revision: 66cd7c255a
 
@@ -903,7 +903,7 @@ nextflow run main.nf -profile my_laptop -resume
 Not only does everything work, but all of the process calls are recognized as having been run previously.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [modest_kay] DSL2 - revision: 328869237b
 
@@ -976,7 +976,7 @@ nextflow run main.nf -profile my_laptop -params-file demo-params.json
 It works! And as expected, this produces the same outputs as previously.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [marvelous_mandelbrot] DSL2 - revision: 328869237b
 
@@ -1126,7 +1126,7 @@ nextflow run main.nf -profile my_laptop,demo
 And it works perfectly!
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [cheesy_shaw] DSL2 - revision: 328869237b
 

docs/hello_nextflow/07_hello_modules.md

@@ -73,7 +73,7 @@ nextflow run main.nf -profile my_laptop,demo
 And so it does.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [special_brenner] DSL2 - revision: 5a07b4894b
 
@@ -220,7 +220,7 @@ nextflow run main.nf -profile my_laptop,demo -resume
 Sure enough, Nextflow recognizes that it's still all the same work to be done, even if the code is split up into multiple files.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [agitated_cuvier] DSL2 - revision: 0ce0cd0c04
 

docs/hello_nextflow/08_hello_nf-test.md

@@ -70,7 +70,7 @@ nextflow run main.nf -profile my_laptop,demo
 This should look very familiar by now if you've been working through this training course from the start.
 
 ```console title="Output"
- N E X T F L O W   ~  version 24.02.0-edge
+ N E X T F L O W   ~  version 24.10.0
 
  ┃ Launching `main.nf` [special_brenner] DSL2 - revision: 5a07b4894b