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RaqManzanovdauwera
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Removed accent from Hola (#933)
* Removed accent from Hola * Revert changes on non-english docs and update note about the tr command being naive Note: Non-english docs will get updated by the translation pipeline * Also update uppercased instances --------- Co-authored-by: Geraldine Van der Auwera <geraldinevdauwera@gmail.com>
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docs/en/docs/hello_nextflow/01_hello_world.md

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Original file line numberDiff line numberDiff line change
@@ -878,7 +878,7 @@ Let's give the `input` parameter a default value by declaring it before the work
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* Pipeline parameters
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*/
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params {
881-
input: String = 'Holà mundo!'
881+
input: String = 'Hola mundo!'
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}
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```
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@@ -888,7 +888,7 @@ Supported types include `String`, `Integer`, `Float`, `Boolean`, and `Path`.
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!!! info
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In older workflows, you may see that whole `params` block written as just `input = 'Holà mundo!'`.
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In older workflows, you may see that whole `params` block written as just `input = 'Hola mundo!'`.
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As you add more parameters to your pipeline, you should add them all to this block, whether or not you need to give them a default value.
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This will make it easy to find all configurable parameters at a glance.
@@ -921,7 +921,7 @@ nextflow run hello-world.nf
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- file : /workspaces/training/hello-nextflow/solutions/1-hello-world/hello-world-3.nf
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- cause: you tried to assign a value to the class 'java.lang.String'
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@ line 24, column 12.
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input: String = 'Holà mundo!'
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input: String = 'Hola mundo!'
925925
^
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1 error
@@ -945,7 +945,7 @@ The output will be in the same place as previously, but the contents should be u
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??? abstract "File contents"
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```console title="results/hello_world/output.txt"
948-
Holà mundo!
948+
Hola mundo!
949949
```
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Nextflow used the default value of the greeting parameter to create the output.

docs/en/docs/hello_nextflow/02_hello_channels.md

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Original file line numberDiff line numberDiff line change
@@ -300,7 +300,7 @@ Workflows typically run on batches of inputs that are meant to be processed in b
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Conveniently, the `channel.of()` channel factory we've been using is quite happy to accept more than one value, so we don't need to modify that at all.
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We can just load multiple values into the channel.
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Let's make them `'Hello'`, `'Bonjour'` and `'Holà'`.
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Let's make them `'Hello'`, `'Bonjour'` and `'Hola'`.
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#### 2.1.1. Add more greetings
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@@ -310,7 +310,7 @@ Before the workflow block, make the following code change:
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```groovy title="hello-channels.nf" linenums="30" hl_lines="2"
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// create a channel for inputs
313-
greeting_ch = channel.of('Hello','Bonjour','Holà')
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greeting_ch = channel.of('Hello','Bonjour','Hola')
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.view()
315315
```
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@@ -343,7 +343,7 @@ nextflow run hello-channels.nf
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[f4/c9962c] process > sayHello (1) [100%] 3 of 3 ✔
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Hello
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Bonjour
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Holà
346+
Hola
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```
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It certainly seems to have run just fine.
@@ -365,7 +365,7 @@ However, there is still only one output in the results directory:
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??? abstract "File contents"
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```console title="results/hello_channels/output.txt"
368-
Holà
368+
Hola
369369
```
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You should see one of the three greetings in there, though the one you got might be different from what is shown here.
@@ -422,7 +422,7 @@ nextflow run hello-channels.nf -ansi-log false
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Launching `hello-channels.nf` [desperate_monod] DSL2 - revision: 59a9a5888a
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Hello
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Bonjour
425-
Holà
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Hola
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[23/871c7e] Submitted process > sayHello (2)
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[7f/21e2c2] Submitted process > sayHello (1)
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[f4/ea10a6] Submitted process > sayHello (3)
@@ -491,7 +491,7 @@ Anyway, now that we have the subdirectories of each process call, we can look fo
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```
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```txt title="work/f4/ea10a680d5687596d3eaa3fcf69272/output.txt"
494-
Holà
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Hola
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```
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This shows that all three processes ran successfully (yay).
@@ -587,7 +587,7 @@ nextflow run hello-channels.nf
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[e8/33ee64] sayHello (2) [100%] 3 of 3 ✔
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Hello
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Bonjour
590-
Holà
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Hola
591591
```
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Reverting back to the summary view, the output is summarized on one line again.
@@ -599,7 +599,7 @@ Have a look at the `results` directory to see if all the output greetings are th
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results/hello_channels/
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├── Bonjour-output.txt
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├── Hello-output.txt
602-
├── Holà-output.txt
602+
├── Hola-output.txt
603603
└── output.txt
604604
```
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@@ -615,8 +615,8 @@ Yes! And they each have the expected contents.
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Hello
616616
```
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```console title="Holà-output.txt"
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Holà
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```console title="Hola-output.txt"
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Hola
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```
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Success! Now we can add as many greetings as we like without worrying about output files being overwritten.
@@ -645,7 +645,7 @@ What if we wanted to provide those multiple inputs in a different way?
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For example, imagine we set up an input variable containing an array of elements like this:
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`greetings_array = ['Hello','Bonjour','Holà']`
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`greetings_array = ['Hello','Bonjour','Hola']`
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Can we load that into our output channel and expect it to work?
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@@ -671,9 +671,9 @@ Let's take the `greetings_array` variable we just imagined and make it a reality
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main:
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// declare an array of input greetings
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greetings_array = ['Hello','Bonjour','Holà']
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greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of('Hello','Bonjour','Holà')
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greeting_ch = channel.of('Hello','Bonjour','Hola')
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.view()
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// emit a greeting
679679
sayHello(greeting_ch)
@@ -690,7 +690,7 @@ Let's take the `greetings_array` variable we just imagined and make it a reality
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main:
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// create a channel for inputs
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greeting_ch = channel.of('Hello','Bonjour','Holà')
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greeting_ch = channel.of('Hello','Bonjour','Hola')
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.view()
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// emit a greeting
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sayHello(greeting_ch)
@@ -704,7 +704,7 @@ This is not yet functional, we've just added a declaration for the array.
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#### 3.1.2. Set array of greetings as the input to the channel factory
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Now we're going to replace the values `'Hello','Bonjour','Holà'` currently hardcoded in the channel factory with the `greetings_array` we just created.
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Now we're going to replace the values `'Hello','Bonjour','Hola'` currently hardcoded in the channel factory with the `greetings_array` we just created.
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In the workflow block, make the following change:
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@@ -715,7 +715,7 @@ In the workflow block, make the following change:
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main:
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// declare an array of input greetings
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greetings_array = ['Hello','Bonjour','Holà']
718+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of(greetings_array)
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.view()
@@ -734,9 +734,9 @@ In the workflow block, make the following change:
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main:
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// declare an array of input greetings
737-
greetings_array = ['Hello','Bonjour','Holà']
737+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of('Hello','Bonjour','Holà')
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greeting_ch = channel.of('Hello','Bonjour','Hola')
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.view()
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// emit a greeting
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sayHello(greeting_ch)
@@ -765,16 +765,16 @@ nextflow run hello-channels.nf
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executor > local (1)
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[a8/1f6ead] sayHello (1) | 0 of 1
768-
[Hello, Bonjour, Holà]
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[Hello, Bonjour, Hola]
769769
ERROR ~ Error executing process > 'sayHello (1)'
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Caused by:
772-
Missing output file(s) `[Hello, Bonjour, Holà]-output.txt` expected by process `sayHello (1)`
772+
Missing output file(s) `[Hello, Bonjour, Hola]-output.txt` expected by process `sayHello (1)`
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Command executed:
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echo '[Hello, Bonjour, Holà]' > '[Hello, Bonjour, Holà]-output.txt'
777+
echo '[Hello, Bonjour, Hola]' > '[Hello, Bonjour, Hola]-output.txt'
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Command exit status:
780780
0
@@ -794,7 +794,7 @@ Oh no! There's an error!
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Look at the output of `view()` and the error messages.
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It looks like Nextflow tried to run a single process call, using `[Hello, Bonjour, Holà]` as a single string value, instead of using the three strings in the array as separate values.
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It looks like Nextflow tried to run a single process call, using `[Hello, Bonjour, Hola]` as a single string value, instead of using the three strings in the array as separate values.
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<figure class="excalidraw">
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--8<-- "docs/en/docs/hello_nextflow/img/hello-channels-array-fail.svg"
@@ -824,7 +824,7 @@ In the workflow block, make the following code change:
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main:
826826
// declare an array of input greetings
827-
greetings_array = ['Hello','Bonjour','Holà']
827+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
829829
greeting_ch = channel.of(greetings_array)
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.view()
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main:
846846
// declare an array of input greetings
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greetings_array = ['Hello','Bonjour','Holà']
847+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of(greetings_array)
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.view()
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879879
main:
880880
// declare an array of input greetings
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greetings_array = ['Hello','Bonjour','Holà']
881+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of(greetings_array)
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.view { greeting -> "Before flatten: $greeting" }
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900900
main:
901901
// declare an array of input greetings
902-
greetings_array = ['Hello','Bonjour','Holà']
902+
greetings_array = ['Hello','Bonjour','Hola']
903903
// create a channel for inputs
904904
greeting_ch = channel.of(greetings_array)
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.view()
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executor > local (3)
947947
[b1/6a1e15] sayHello (2) [100%] 3 of 3 ✔
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Before flatten: [Hello, Bonjour, Holà]
948+
Before flatten: [Hello, Bonjour, Hola]
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After flatten: Hello
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After flatten: Bonjour
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After flatten: Holà
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After flatten: Hola
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```
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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.
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```csv title="data/greetings.csv" linenums="1"
985985
Hello,English,123
986986
Bonjour,French,456
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Holà,Spanish,789
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Hola,Spanish,789
988988
```
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Our next task is to adapt our workflow to read in the values from this file.
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/*
10271027
* Pipeline parameters
10281028
*/
1029-
input: String = 'Holà mundo!'
1029+
input: String = 'Hola mundo!'
10301030
```
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This assumes the file is co-located with the workflow code.
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10661066
main:
10671067
// declare an array of input greetings
1068-
greetings_array = ['Hello','Bonjour','Holà']
1068+
greetings_array = ['Hello','Bonjour','Hola']
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// create a channel for inputs
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greeting_ch = channel.of(greetings_array)
10711071
.view { greeting -> "Before flatten: $greeting" }
@@ -1205,7 +1205,7 @@ nextflow run hello-channels.nf
12051205
Before splitCsv: /workspaces/training/hello-nextflow/data/greetings.csv
12061206
After splitCsv: [Hello, English, 123]
12071207
After splitCsv: [Bonjour, French, 456]
1208-
After splitCsv: [Holà, Spanish, 789]
1208+
After splitCsv: [Hola, Spanish, 789]
12091209
ERROR ~ Error executing process > 'sayHello (2)'
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12111211
Caused by:
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13251325
Before splitCsv: /workspaces/training/hello-nextflow/data/greetings.csv
13261326
After splitCsv: [Hello, English, 123]
13271327
After splitCsv: [Bonjour, French, 456]
1328-
After splitCsv: [Holà, Spanish, 789]
1328+
After splitCsv: [Hola, Spanish, 789]
13291329
After map: Hello
13301330
After map: Bonjour
1331-
After map: Holà
1331+
After map: Hola
13321332
```
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13341334
This time it should run without error.

docs/en/docs/hello_nextflow/03_hello_workflow.md

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Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ For this chapter, it's under `results/hello_workflow/`.
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results/hello_workflow
8383
├── Bonjour-output.txt
8484
├── Hello-output.txt
85-
└── Holà-output.txt
85+
└── Hola-output.txt
8686
```
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8888
If that worked for you, you're ready to learn how to assemble a multi-step workflow.
@@ -111,7 +111,7 @@ To do the conversion of the greetings to uppercase, we're going to use a classic
111111
tr '[a-z]' '[A-Z]'
112112
```
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114-
This is a very naive text replacement one-liner that does not account for accented letters, so for example 'Holà' will become 'HOLà', but it will do a good enough job for demonstrating the Nextflow concepts and that's what matters.
114+
This is a very naive text replacement one-liner that does not account for accented letters, but it will do a good enough job for demonstrating the Nextflow concepts and that's what matters.
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116116
To test it out, we can run the `echo 'Hello World'` command and pipe its output to the `tr` command:
117117

@@ -328,10 +328,10 @@ You'll find the outputs in the `results/hello_workflow` directory as set in the
328328
results/hello_workflow/
329329
├── Bonjour-output.txt
330330
├── Hello-output.txt
331-
├── Holà-output.txt
331+
├── Hola-output.txt
332332
├── UPPER-Bonjour-output.txt
333333
├── UPPER-Hello-output.txt
334-
└── UPPER-Holà-output.txt
334+
└── UPPER-Hola-output.txt
335335
```
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That's convenient! But it's still worth taking a look inside the work directory of one of the calls to the second process.
@@ -340,8 +340,8 @@ That's convenient! But it's still worth taking a look inside the work directory
340340

341341
```console
342342
work/e0/ecf81b4cacc648b9b994218d5b29d7/
343-
├── Holà-output.txt -> /workspaces/training/hello-nextflow/work/ab/81632178cd37e9e815959278808819/Holà-output.txt
344-
└── UPPER-Holà-output.txt
343+
├── Hola-output.txt -> /workspaces/training/hello-nextflow/work/ab/81632178cd37e9e815959278808819/Hola-output.txt
344+
└── UPPER-Hola-output.txt
345345
```
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347347
Notice there are two `*-output` files: the output of the first process as well as the output of the second.
@@ -389,8 +389,8 @@ Run the following in your terminal:
389389
```bash
390390
echo 'Hello' | tr '[a-z]' '[A-Z]' > UPPER-Hello-output.txt
391391
echo 'Bonjour' | tr '[a-z]' '[A-Z]' > UPPER-Bonjour-output.txt
392-
echo 'Holà' | tr '[a-z]' '[A-Z]' > UPPER-Holà-output.txt
393-
cat UPPER-Hello-output.txt UPPER-Bonjour-output.txt UPPER-Holà-output.txt > COLLECTED-output.txt
392+
echo 'Hola' | tr '[a-z]' '[A-Z]' > UPPER-Hola-output.txt
393+
cat UPPER-Hello-output.txt UPPER-Bonjour-output.txt UPPER-Hola-output.txt > COLLECTED-output.txt
394394
```
395395

396396
The output is a text file called `COLLECTED-output.txt` that contains the uppercase versions of the original greetings.
@@ -565,7 +565,7 @@ Now have a look at the contents of the final output file.
565565
??? abstract "File contents"
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567567
```console title="results/COLLECTED-output.txt"
568-
Holà
568+
Hola
569569
```
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571571
Oh no. The collection step was run individually on each greeting, which is NOT what we wanted.
@@ -653,8 +653,8 @@ nextflow run hello-workflow.nf -resume
653653
[1e/83586c] collectGreetings | 1 of 1 ✔
654654
Before collect: /workspaces/training/hello-nextflow/work/b3/d52708edba8b864024589285cb3445/UPPER-Bonjour-output.txt
655655
Before collect: /workspaces/training/hello-nextflow/work/99/79394f549e3040dfc2440f69ede1fc/UPPER-Hello-output.txt
656-
Before collect: /workspaces/training/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Holà-output.txt
657-
After collect: [/workspaces/training/hello-nextflow/work/b3/d52708edba8b864024589285cb3445/UPPER-Bonjour-output.txt, /workspaces/training/hello-nextflow/work/99/79394f549e3040dfc2440f69ede1fc/UPPER-Hello-output.txt, /workspaces/training/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Holà-output.txt]
656+
Before collect: /workspaces/training/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Hola-output.txt
657+
After collect: [/workspaces/training/hello-nextflow/work/b3/d52708edba8b864024589285cb3445/UPPER-Bonjour-output.txt, /workspaces/training/hello-nextflow/work/99/79394f549e3040dfc2440f69ede1fc/UPPER-Hello-output.txt, /workspaces/training/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Hola-output.txt]
658658
```
659659

660660
It runs successfully, although the log output may look a little messier than this (we cleaned it up for readability).

docs/en/docs/hello_nextflow/04_hello_modules.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -86,11 +86,11 @@ As previously, you will find the output files in the directory specified in the
8686
├── Bonjour-output.txt
8787
├── COLLECTED-batch-output.txt
8888
├── Hello-output.txt
89-
├── Holà-output.txt
89+
├── Hola-output.txt
9090
├── batch-report.txt
9191
├── UPPER-Bonjour-output.txt
9292
├── UPPER-Hello-output.txt
93-
└── UPPER-Holà-output.txt
93+
└── UPPER-Hola-output.txt
9494
```
9595

9696
If that worked for you, you're ready to learn how to modularize your workflow code.

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