diff --git a/docs/hello_nextflow/01_hello_world.md b/docs/hello_nextflow/01_hello_world.md index 20253a018..8182537ee 100644 --- a/docs/hello_nextflow/01_hello_world.md +++ b/docs/hello_nextflow/01_hello_world.md @@ -210,7 +210,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-world.nf` [goofy_torvalds] DSL2 - revision: c33d41f479 @@ -351,7 +351,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-world.nf` [jovial_mayer] DSL2 - revision: 35bd3425e5 @@ -395,7 +395,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-world.nf` [golden_cantor] DSL2 - revision: 35bd3425e5 @@ -584,7 +584,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-world.nf` [elated_lavoisier] DSL2 - revision: 7c031b42ea @@ -637,7 +637,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-world.nf` [determined_edison] DSL2 - revision: 3539118582 @@ -666,7 +666,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 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 87c2ad6a5..c7fe84781 100644 --- a/docs/hello_nextflow/02_hello_channels.md +++ b/docs/hello_nextflow/02_hello_channels.md @@ -35,7 +35,7 @@ nextflow run hello-channels.nf --greeting 'Hello Channels!' ``` ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [insane_lichterman] DSL2 - revision: c33d41f479 @@ -149,7 +149,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [nice_heisenberg] DSL2 - revision: 41b4aeb7e9 @@ -219,7 +219,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [suspicious_lamport] DSL2 - revision: 778deadaea @@ -244,7 +244,7 @@ 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 24.10.0 +N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [pensive_poitras] DSL2 - revision: 778deadaea [76/f61695] Submitted process > sayHello (1) [6e/d12e35] Submitted process > sayHello (3) @@ -354,7 +354,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [astonishing_bell] DSL2 - revision: f57ff44a69 @@ -478,7 +478,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [friendly_koch] DSL2 - revision: 97256837a7 @@ -580,7 +580,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [tiny_elion] DSL2 - revision: 1d834f23d2 @@ -697,7 +697,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [adoring_bhabha] DSL2 - revision: 8ce25edc39 @@ -764,7 +764,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-channels.nf` [stoic_ride] DSL2 - revision: a0e5de507e @@ -852,7 +852,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 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 e455b295d..1b36fdd04 100644 --- a/docs/hello_nextflow/03_hello_workflow.md +++ b/docs/hello_nextflow/03_hello_workflow.md @@ -40,7 +40,7 @@ nextflow run hello-workflow.nf ``` ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-workflow.nf` [stupefied_sammet] DSL2 - revision: b9e466930b @@ -197,7 +197,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-workflow.nf` [disturbed_darwin] DSL2 - revision: 4e252c048f @@ -420,7 +420,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-workflow.nf` [mad_gilbert] DSL2 - revision: 6acfd5e28d @@ -511,7 +511,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-workflow.nf` [soggy_franklin] DSL2 - revision: bc8e1b2726 @@ -691,7 +691,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-workflow.nf` [confident_rutherford] DSL2 - revision: bc58af409c @@ -842,7 +842,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 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 ab18757f9..e9d89beaf 100644 --- a/docs/hello_nextflow/04_hello_modules.md +++ b/docs/hello_nextflow/04_hello_modules.md @@ -37,7 +37,7 @@ nextflow run hello-modules.nf ``` ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-modules.nf` [festering_nobel] DSL2 - revision: eeca64cdb1 @@ -168,7 +168,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-modules.nf` [romantic_poisson] DSL2 - revision: 96edfa9ad3 @@ -265,7 +265,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-modules.nf` [nauseous_heisenberg] DSL2 - revision: a04a9f2da0 @@ -357,7 +357,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 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 a3ed70bcf..a93ec321c 100644 --- a/docs/hello_nextflow/05_hello_containers.md +++ b/docs/hello_nextflow/05_hello_containers.md @@ -38,7 +38,7 @@ nextflow run hello-containers.nf This should produce the following output: ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-containers.nf` [tender_becquerel] DSL2 - revision: f7cat8e223 @@ -187,7 +187,7 @@ ls / ``` ```console title="Output" -bin dev etc home lib media mnt opt proc root run sbin srv sys tmp usr var +bin boot dev etc home lib lib64 media mnt opt proc root run sbin srv sys tmp usr var ``` You can see that the filesystem inside the container is different from the filesystem on your host system. @@ -277,8 +277,8 @@ ls /data Depending on what part of this training you've done before, the output below my look slightly different. ```console title="Output" -demo-params.json hello-channels.nf hello-workflow.nf modules results -greetings.csv hello-modules.nf hello-world.nf nextflow.config work +greetings.csv hello-config.nf hello-modules.nf hello-world.nf nextflow.config solutions work +hello-channels.nf hello-containers.nf hello-workflow.nf modules results test-params.json ``` @@ -498,7 +498,7 @@ nextflow run hello-containers.nf -resume Oh no, there's an error! ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-containers.nf` [special_lovelace] DSL2 - revision: 028a841db1 @@ -599,7 +599,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 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 7410c51c4..43054a7ac 100644 --- a/docs/hello_nextflow/06_hello_config.md +++ b/docs/hello_nextflow/06_hello_config.md @@ -42,7 +42,7 @@ nextflow run hello-config.nf ``` ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-config.nf` [reverent_heisenberg] DSL2 - revision: 028a841db1 @@ -145,7 +145,7 @@ nextflow run hello-config.nf This should work without issue. ```console title="Output" - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-config.nf` [trusting_lovelace] DSL2 - revision: 028a841db1 @@ -360,7 +360,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-config.nf` [disturbed_sammet] DSL2 - revision: ede9037d02 @@ -509,7 +509,7 @@ nextflow run hello-config.nf -profile my_laptop This still produces the following output: ``` - N E X T F L O W ~ version 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02 @@ -591,7 +591,7 @@ 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 24.10.0 + N E X T F L O W ~ version 25.04.3 Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02 diff --git a/hello-nextflow/hello-containers.nf b/hello-nextflow/hello-containers.nf index 8764606bf..4ba435eda 100644 --- a/hello-nextflow/hello-containers.nf +++ b/hello-nextflow/hello-containers.nf @@ -28,5 +28,5 @@ workflow { collectGreetings(convertToUpper.out.collect(), params.batch) // emit a message about the size of the batch - collectGreetings.out.count.view { "There were $it greetings in this batch" } + collectGreetings.out.count.view { num_greetings -> "There were $num_greetings greetings in this batch" } }