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