diff --git a/.devcontainer/codespaces-dev/devcontainer.json b/.devcontainer/codespaces-dev/devcontainer.json
index b739415e6c..98853d73d9 100644
--- a/.devcontainer/codespaces-dev/devcontainer.json
+++ b/.devcontainer/codespaces-dev/devcontainer.json
@@ -29,7 +29,7 @@
// Nextflow installation version
"NXF_HOME": "/workspaces/.nextflow",
"NXF_EDGE": "0",
- "NXF_VER": "25.04.3",
+ "NXF_VER": "25.04.6",
// Other env vars
"HOST_PROJECT_PATH": "/workspaces/training",
"SHELL": "/bin/bash" // Ush bash
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index be11210961..041821025b 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -12,7 +12,7 @@
// Nextflow installation version
"NXF_HOME": "/workspaces/.nextflow",
"NXF_EDGE": "0",
- "NXF_VER": "25.04.3",
+ "NXF_VER": "25.04.6",
// Other env vars
"HOST_PROJECT_PATH": "/workspaces/training",
"SHELL": "/bin/bash" // Ush bash
diff --git a/.devcontainer/local-dev/devcontainer.json b/.devcontainer/local-dev/devcontainer.json
index 3ab026df46..dddbd40911 100644
--- a/.devcontainer/local-dev/devcontainer.json
+++ b/.devcontainer/local-dev/devcontainer.json
@@ -30,7 +30,7 @@
// Nextflow installation version
"NXF_HOME": "/workspaces/training/.nextflow",
"NXF_EDGE": "0",
- "NXF_VER": "25.04.3",
+ "NXF_VER": "25.04.6",
// Other env vars
"HOST_PROJECT_PATH": "/workspaces/training",
"SHELL": "/bin/bash" // Ush bash
diff --git a/docs/hello_nextflow/01_hello_world.md b/docs/hello_nextflow/01_hello_world.md
index a9403ceea0..bffa6265f7 100644
--- a/docs/hello_nextflow/01_hello_world.md
+++ b/docs/hello_nextflow/01_hello_world.md
@@ -212,7 +212,7 @@ nextflow run hello-world.nf
You console output should look something like this:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [goofy_torvalds] DSL2 - revision: c33d41f479
@@ -353,7 +353,7 @@ nextflow run hello-world.nf
The log output should look very familiar:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [jovial_mayer] DSL2 - revision: 35bd3425e5
@@ -397,7 +397,7 @@ nextflow run hello-world.nf -resume
The console output should look similar.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [golden_cantor] DSL2 - revision: 35bd3425e5
@@ -586,7 +586,7 @@ nextflow run hello-world.nf --greeting 'Bonjour le monde!'
If you made all three edits correctly, you should get another successful execution:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [elated_lavoisier] DSL2 - revision: 7c031b42ea
@@ -639,7 +639,7 @@ nextflow run hello-world.nf
The console output should look the same.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [determined_edison] DSL2 - revision: 3539118582
@@ -668,7 +668,7 @@ nextflow run hello-world.nf --greeting 'Konnichiwa!'
The console output should look the same.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-world.nf` [elegant_faraday] DSL2 - revision: 3539118582
diff --git a/docs/hello_nextflow/02_hello_channels.md b/docs/hello_nextflow/02_hello_channels.md
index c8c5e179bf..5a5bfb99b7 100644
--- a/docs/hello_nextflow/02_hello_channels.md
+++ b/docs/hello_nextflow/02_hello_channels.md
@@ -37,7 +37,7 @@ nextflow run hello-channels.nf --greeting 'Hello Channels!'
```
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [insane_lichterman] DSL2 - revision: c33d41f479
@@ -151,7 +151,7 @@ nextflow run hello-channels.nf
If you made both edits correctly, you should get another successful execution:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [nice_heisenberg] DSL2 - revision: 41b4aeb7e9
@@ -221,7 +221,7 @@ nextflow run hello-channels.nf
It certainly seems to run just fine:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [suspicious_lamport] DSL2 - revision: 778deadaea
@@ -246,7 +246,7 @@ nextflow run hello-channels.nf -ansi-log false
This time we see all three process runs and their associated work subdirectories listed in the output:
```console title="Output" linenums="1"
-N E X T F L O W ~ version 25.04.3
+N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [pensive_poitras] DSL2 - revision: 778deadaea
[76/f61695] Submitted process > sayHello (1)
[6e/d12e35] Submitted process > sayHello (3)
@@ -356,7 +356,7 @@ nextflow run hello-channels.nf
Reverting back to the summary view, the output looks like this again:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [astonishing_bell] DSL2 - revision: f57ff44a69
@@ -480,7 +480,7 @@ nextflow run hello-channels.nf
Oh no! Nextflow throws an error that starts like this:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [friendly_koch] DSL2 - revision: 97256837a7
@@ -582,7 +582,7 @@ nextflow run hello-channels.nf
This time it works AND gives us the additional insight into what the contents of the channel look like before and after we run the `flatten()` operator:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [tiny_elion] DSL2 - revision: 1d834f23d2
@@ -699,7 +699,7 @@ nextflow run hello-channels.nf
Oh no, it doesn't work. Here's the start of the console output and error message:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [adoring_bhabha] DSL2 - revision: 8ce25edc39
@@ -766,7 +766,7 @@ nextflow run hello-channels.nf
Interestingly, this fails too, but with a different error. The console output and error starts like this:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [stoic_ride] DSL2 - revision: a0e5de507e
@@ -854,7 +854,7 @@ nextflow run hello-channels.nf
This time it should run without error.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-channels.nf` [tiny_heisenberg] DSL2 - revision: 845b471427
diff --git a/docs/hello_nextflow/03_hello_workflow.md b/docs/hello_nextflow/03_hello_workflow.md
index d5bcd340cd..34948f2b53 100644
--- a/docs/hello_nextflow/03_hello_workflow.md
+++ b/docs/hello_nextflow/03_hello_workflow.md
@@ -42,7 +42,7 @@ nextflow run hello-workflow.nf
```
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [stupefied_sammet] DSL2 - revision: b9e466930b
@@ -199,7 +199,7 @@ nextflow run hello-workflow.nf -resume
You should see the following output:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [disturbed_darwin] DSL2 - revision: 4e252c048f
@@ -422,7 +422,7 @@ nextflow run hello-workflow.nf -resume
It runs successfully, including the third step:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [mad_gilbert] DSL2 - revision: 6acfd5e28d
@@ -513,7 +513,7 @@ nextflow run hello-workflow.nf -resume
It runs successfully, although the log output may look a little messier than this (we cleaned it up for readability).
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [soggy_franklin] DSL2 - revision: bc8e1b2726
@@ -693,7 +693,7 @@ nextflow run hello-workflow.nf -resume --batch trio
It runs successfully:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [confident_rutherford] DSL2 - revision: bc58af409c
@@ -844,7 +844,7 @@ nextflow run hello-workflow.nf -resume --batch trio
This runs successfully:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-workflow.nf` [evil_sinoussi] DSL2 - revision: eeca64cdb1
diff --git a/docs/hello_nextflow/04_hello_modules.md b/docs/hello_nextflow/04_hello_modules.md
index cc2476a6b4..4655def0cf 100644
--- a/docs/hello_nextflow/04_hello_modules.md
+++ b/docs/hello_nextflow/04_hello_modules.md
@@ -39,7 +39,7 @@ nextflow run hello-modules.nf
```
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-modules.nf` [festering_nobel] DSL2 - revision: eeca64cdb1
@@ -170,7 +170,7 @@ nextflow run hello-modules.nf -resume
This runs quickly very quickly because everything is cached.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-modules.nf` [romantic_poisson] DSL2 - revision: 96edfa9ad3
@@ -267,7 +267,7 @@ nextflow run hello-modules.nf -resume
This should still produce the same output as previously.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-modules.nf` [nauseous_heisenberg] DSL2 - revision: a04a9f2da0
@@ -359,7 +359,7 @@ nextflow run hello-modules.nf -resume
This should still produce the same output as previously.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-modules.nf` [friendly_coulomb] DSL2 - revision: 7aa2b9bc0f
diff --git a/docs/hello_nextflow/05_hello_containers.md b/docs/hello_nextflow/05_hello_containers.md
index eaaade723a..eb5c4ddf1f 100644
--- a/docs/hello_nextflow/05_hello_containers.md
+++ b/docs/hello_nextflow/05_hello_containers.md
@@ -40,7 +40,7 @@ nextflow run hello-containers.nf
This should produce the following output:
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-containers.nf` [tender_becquerel] DSL2 - revision: f7cat8e223
@@ -500,7 +500,7 @@ nextflow run hello-containers.nf -resume
Oh no, there's an error!
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-containers.nf` [special_lovelace] DSL2 - revision: 028a841db1
@@ -601,7 +601,7 @@ nextflow run hello-containers.nf -resume
This time it does indeed work.
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-containers.nf` [elegant_brattain] DSL2 - revision: 028a841db1
diff --git a/docs/hello_nextflow/06_hello_config.md b/docs/hello_nextflow/06_hello_config.md
index a8c7225811..b2d7691ac3 100644
--- a/docs/hello_nextflow/06_hello_config.md
+++ b/docs/hello_nextflow/06_hello_config.md
@@ -44,7 +44,7 @@ nextflow run hello-config.nf
```
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-config.nf` [reverent_heisenberg] DSL2 - revision: 028a841db1
@@ -147,7 +147,7 @@ nextflow run hello-config.nf
This should work without issue.
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-config.nf` [trusting_lovelace] DSL2 - revision: 028a841db1
@@ -362,7 +362,7 @@ nextflow run hello-config.nf -params-file test-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 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-config.nf` [disturbed_sammet] DSL2 - revision: ede9037d02
@@ -511,7 +511,7 @@ nextflow run hello-config.nf -profile my_laptop
This still produces the following output:
```
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02
@@ -593,7 +593,7 @@ nextflow run hello-config.nf -profile my_laptop,test
This should produce the following:
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02
diff --git a/docs/nextflow_run/01_basics.md b/docs/nextflow_run/01_basics.md
index 53891e1705..a77a7c578a 100644
--- a/docs/nextflow_run/01_basics.md
+++ b/docs/nextflow_run/01_basics.md
@@ -81,7 +81,7 @@ nextflow run 1-hello.nf --greeting 'Hello World!'
You console output should look something like this:
```console title="Output" linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `1-hello.nf` [goofy_torvalds] DSL2 - revision: c33d41f479
@@ -423,7 +423,7 @@ The console output should look similar.
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `1-hello.nf` [tiny_noyce] DSL2 - revision: c33d41f479
diff --git a/docs/nextflow_run/02_pipeline.md b/docs/nextflow_run/02_pipeline.md
index 2d193e5160..a6191e468e 100644
--- a/docs/nextflow_run/02_pipeline.md
+++ b/docs/nextflow_run/02_pipeline.md
@@ -51,7 +51,7 @@ This should run without error.
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `2a-inputs.nf` [mighty_sammet] DSL2 - revision: 29fb5352b3
@@ -141,7 +141,7 @@ This time we see all three process runs and their associated work subdirectories
Command output
```console linenums="1"
-N E X T F L O W ~ version 25.04.3
+N E X T F L O W ~ version 25.04.6
Launching `2a-inputs.nf` [pedantic_hamilton] DSL2 - revision: 6bbc42e49f
[ab/1a8ece] Submitted process > sayHello (1)
[0d/2cae24] Submitted process > sayHello (2)
@@ -357,7 +357,7 @@ Once again this should run successfully.
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `2b-multistep.nf` [soggy_franklin] DSL2 - revision: bc8e1b2726
@@ -696,7 +696,7 @@ Once again this should run successfully.
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `2c-modules.nf` [soggy_franklin] DSL2 - revision: bc8e1b2726
@@ -1073,7 +1073,7 @@ This should work without error.
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `2d-container.nf` [elegant_brattain] DSL2 - revision: 028a841db1
diff --git a/docs/nextflow_run/03_config.md b/docs/nextflow_run/03_config.md
index 751adffb7f..8f01aa9efd 100644
--- a/docs/nextflow_run/03_config.md
+++ b/docs/nextflow_run/03_config.md
@@ -102,7 +102,7 @@ This should work without error.
Command output
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `3-main.nf` [trusting_lovelace] DSL2 - revision: 028a841db1
@@ -441,7 +441,7 @@ This will produce the same output, but is more convenient to type, especially wh
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `3-main.nf` [wise_mahavira] DSL2 - revision: 356df0818d
@@ -533,7 +533,7 @@ This will create a new set of directories under `tux-run/` including `tux-run/wo
Command output
```console linenums="1"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `../3-main.nf` [trusting_escher] DSL2 - revision: 356df0818d
@@ -612,7 +612,7 @@ This should run without error.
Command output
```console title="Output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `3-main.nf` [disturbed_sammet] DSL2 - revision: ede9037d02
@@ -719,7 +719,7 @@ This should run without error and produce the same results as previously.
Command output
```console
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `3-main.nf` [gigantic_brazil] DSL2 - revision: ede9037d02
@@ -804,7 +804,7 @@ This should run without error.
Command output
```console
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `3-main.nf` [gigantic_brazil] DSL2 - revision: ede9037d02
diff --git a/docs/side_quests/debugging.md b/docs/side_quests/debugging.md
index d2e8e6ef29..1c5147728f 100644
--- a/docs/side_quests/debugging.md
+++ b/docs/side_quests/debugging.md
@@ -112,7 +112,7 @@ nextflow run bad_syntax.nf
You'll see an error message like this:
```console title="Syntax error output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `bad_syntax.nf` [stupefied_bhabha] DSL2 - revision: ca6327fad2
@@ -228,7 +228,7 @@ nextflow run invalid_process.nf
You'll see an error like:
```console title="Invalid process keyword error"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `invalid_process.nf` [nasty_jepsen] DSL2 - revision: da9758d614
@@ -528,7 +528,7 @@ nextflow run badpractice_syntax.nf
When you run this workflow, it will execute successfully:
```console title="Successful execution despite bad practice"
-N E X T F L O W ~ version 25.04.3
+N E X T F L O W ~ version 25.04.6
Launching `badpractice_syntax.nf` [peaceful_euler] DSL2 - revision: 7b2c9a1d45
@@ -638,7 +638,7 @@ nextflow run bad_number_inputs.nf
```
```console title="Wrong number of channels error"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `bad_number_inputs.nf` [high_mendel] DSL2 - revision: 955705c51b
@@ -734,7 +734,7 @@ nextflow run exhausted.nf
When you run this workflow, it will execute without error, processing a single sample:
```console title="Exhausted channel output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `exhausted.nf` [extravagant_gauss] DSL2 - revision: 08cff7ba2a
@@ -993,7 +993,7 @@ nextflow run bad_channel_shape_viewed.nf
You'll see output like this:
```console title="Channel debugging output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `bad_channel_shape_viewed.nf` [maniac_poisson] DSL2 - revision: b4f24dc9da
@@ -1082,7 +1082,7 @@ nextflow run missing_output.nf
You'll see an error like this:
```console title="Missing output files error"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `missing_output.nf` [zen_stone] DSL2 - revision: 37ff61f926
@@ -1497,7 +1497,7 @@ nextflow run bad_channel_shape_viewed_debug.nf
You will see output like this:
```console title="Real-time process output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `bad_channel_shape_viewed_debug.nf` [agitated_crick] DSL2 - revision: ea3676d9ec
@@ -1561,7 +1561,7 @@ nextflow run bad_syntax.nf -preview
You'll see output like this:
```console title="Preview mode output"
- N E X T F L O W ~ version 25.04.3
+ N E X T F L O W ~ version 25.04.6
Launching `bad_syntax.nf` [sick_fermi] DSL2 - revision: ca6327fad2