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Update nextflow to 25.04.6 #646

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8e3f66b
Update Nextflow version to 25.04.06 in devcontainer configurations
cursoragent Aug 6, 2025
30a12c5
Update Nextflow version from 25.04.3 to 25.04.6 across documentation
cursoragent Aug 6, 2025
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2 changes: 1 addition & 1 deletion .devcontainer/codespaces-dev/devcontainer.json
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .devcontainer/devcontainer.json
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .devcontainer/local-dev/devcontainer.json
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Expand Up @@ -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
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12 changes: 6 additions & 6 deletions docs/hello_nextflow/01_hello_world.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

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20 changes: 10 additions & 10 deletions docs/hello_nextflow/02_hello_channels.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand All @@ -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)
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down
12 changes: 6 additions & 6 deletions docs/hello_nextflow/03_hello_workflow.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down
8 changes: 4 additions & 4 deletions docs/hello_nextflow/04_hello_modules.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down
6 changes: 3 additions & 3 deletions docs/hello_nextflow/05_hello_containers.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down
10 changes: 5 additions & 5 deletions docs/hello_nextflow/06_hello_config.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down
4 changes: 2 additions & 2 deletions docs/nextflow_run/01_basics.md
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Expand Up @@ -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

Expand Down Expand Up @@ -423,7 +423,7 @@ The console output should look similar.
<summary>Command output</summary>

```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

Expand Down
10 changes: 5 additions & 5 deletions docs/nextflow_run/02_pipeline.md
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Expand Up @@ -51,7 +51,7 @@ This should run without error.
<summary>Command output</summary>

```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

Expand Down Expand Up @@ -141,7 +141,7 @@ This time we see all three process runs and their associated work subdirectories
<summary>Command output</summary>

```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)
Expand Down Expand Up @@ -357,7 +357,7 @@ Once again this should run successfully.
<summary>Command output</summary>

```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

Expand Down Expand Up @@ -696,7 +696,7 @@ Once again this should run successfully.
<summary>Command output</summary>

```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

Expand Down Expand Up @@ -1073,7 +1073,7 @@ This should work without error.
<summary>Command output</summary>

```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

Expand Down
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