Update file paths with gitpod

Author: ewels

docs/advanced/structure.md

@@ -92,7 +92,7 @@ You'll notice a `nxf_container_env` bash function that appends our bin directory
 ```bash
 nxf_container_env() {
 cat << EOF
-export PATH="\$PATH:/workspace/gitpod/nf-training/advanced/structure/bin"
+export PATH="\$PATH:/workspaces/training/nf-training-advanced/structure/bin"
 EOF
 }
 ```

docs/basic_training/channels.md

@@ -324,9 +324,9 @@ Channel
 It will produce an output similar to the following:
 
 ```console title="Output"
-[liver, [/workspace/gitpod/nf-training/data/ggal/liver_1.fq, /workspace/gitpod/nf-training/data/ggal/liver_2.fq]]
-[gut, [/workspace/gitpod/nf-training/data/ggal/gut_1.fq, /workspace/gitpod/nf-training/data/ggal/gut_2.fq]]
-[lung, [/workspace/gitpod/nf-training/data/ggal/lung_1.fq, /workspace/gitpod/nf-training/data/ggal/lung_2.fq]]
+[liver, [/workspaces/training/nf-training/data/ggal/liver_1.fq, /workspaces/training/nf-training/data/ggal/liver_2.fq]]
+[gut, [/workspaces/training/nf-training/data/ggal/gut_1.fq, /workspaces/training/nf-training/data/ggal/gut_2.fq]]
+[lung, [/workspaces/training/nf-training/data/ggal/lung_1.fq, /workspaces/training/nf-training/data/ggal/lung_2.fq]]
 ```
 
 !!! warning

docs/basic_training/channels.pt.md

@@ -229,9 +229,9 @@ Channel
 Ele produzirá uma saída semelhante à seguinte:
 
 ```groovy
-[liver, [/workspace/gitpod/nf-training/data/ggal/liver_1.fq, /workspace/gitpod/nf-training/data/ggal/liver_2.fq]]
-[gut, [/workspace/gitpod/nf-training/data/ggal/gut_1.fq, /workspace/gitpod/nf-training/data/ggal/gut_2.fq]]
-[lung, [/workspace/gitpod/nf-training/data/ggal/lung_1.fq, /workspace/gitpod/nf-training/data/ggal/lung_2.fq]]
+[liver, [/workspaces/training/nf-training/data/ggal/liver_1.fq, /workspaces/training/nf-training/data/ggal/liver_2.fq]]
+[gut, [/workspaces/training/nf-training/data/ggal/gut_1.fq, /workspaces/training/nf-training/data/ggal/gut_2.fq]]
+[lung, [/workspaces/training/nf-training/data/ggal/lung_1.fq, /workspaces/training/nf-training/data/ggal/lung_2.fq]]
 ```
 
 !!! warning
@@ -487,7 +487,7 @@ for (List linha : linhas) {
         Adicione um arquivo de texto CSV contendo o seguinte, como uma entrada de exemplo com o nome "fastq.csv":
 
         ```csv
-        gut,/workspace/gitpod/nf-training/data/ggal/gut_1.fq,/workspace/gitpod/nf-training/data/ggal/gut_2.fq
+        gut,/workspaces/training/nf-training/data/ggal/gut_1.fq,/workspaces/training/nf-training/data/ggal/gut_2.fq
         ```
 
         Em seguida, substitua o canal de entrada para as leituras em `script7.nf`, alterando as seguintes linhas:

docs/basic_training/containers.md

@@ -248,7 +248,7 @@ docker run --volume $PWD:$PWD --workdir $PWD my-image \
 Or set a folder you want to mount as an environmental variable, called `DATA`:
 
 ```bash
-DATA=/workspace/gitpod/nf-training/data
+DATA=/workspaces/training/nf-training/data
 docker run --volume $DATA:$DATA --workdir $PWD my-image \
     salmon index -t $PWD/data/ggal/transcriptome.fa -i transcript-index
 ```

docs/basic_training/containers.pt.md

@@ -181,7 +181,7 @@ docker run --volume $PWD:$PWD --workdir $PWD minha-imagem \
 Ou definir uma pasta que você queira montar como uma variável de ambiente, chamada `DATA`:
 
 ```bash
-DATA=/workspace/gitpod/nf-training/data
+DATA=/workspaces/training/nf-training/data
 docker run --volume $DATA:$DATA --workdir $PWD minha-imagem \
     salmon index -t $PWD/data/ggal/transcriptome.fa -i transcript-index
 ```

docs/basic_training/operators.md

@@ -135,12 +135,12 @@ Channel
         Your output should look like this:
 
         ```console title="Output"
-        [gut_1.fq, /workspace/gitpod/nf-training/data/ggal/gut_1.fq]
-        [gut_2.fq, /workspace/gitpod/nf-training/data/ggal/gut_2.fq]
-        [liver_1.fq, /workspace/gitpod/nf-training/data/ggal/liver_1.fq]
-        [liver_2.fq, /workspace/gitpod/nf-training/data/ggal/liver_2.fq]
-        [lung_1.fq, /workspace/gitpod/nf-training/data/ggal/lung_1.fq]
-        [lung_2.fq, /workspace/gitpod/nf-training/data/ggal/lung_2.fq]
+        [gut_1.fq, /workspaces/training/nf-training/data/ggal/gut_1.fq]
+        [gut_2.fq, /workspaces/training/nf-training/data/ggal/gut_2.fq]
+        [liver_1.fq, /workspaces/training/nf-training/data/ggal/liver_1.fq]
+        [liver_2.fq, /workspaces/training/nf-training/data/ggal/liver_2.fq]
+        [lung_1.fq, /workspaces/training/nf-training/data/ggal/lung_1.fq]
+        [lung_2.fq, /workspaces/training/nf-training/data/ggal/lung_2.fq]
         ```
 
 ### `mix()`
@@ -248,11 +248,11 @@ This operator is especially useful to process a group together with all the elem
         ```
 
         ```console title="Output"
-        [patients_1, [/workspace/gitpod/nf-training/data/meta/patients_1.csv]]
-        [patients_2, [/workspace/gitpod/nf-training/data/meta/patients_2.csv]]
-        [random, [/workspace/gitpod/nf-training/data/meta/random.txt]]
-        [regions, [/workspace/gitpod/nf-training/data/meta/regions.json, /workspace/gitpod/nf-training/data/meta/regions.tsv, /workspace/gitpod/nf-training/data/meta/regions.yml]]
-        [regions2, [/workspace/gitpod/nf-training/data/meta/regions2.json]]
+        [patients_1, [/workspaces/training/nf-training/data/meta/patients_1.csv]]
+        [patients_2, [/workspaces/training/nf-training/data/meta/patients_2.csv]]
+        [random, [/workspaces/training/nf-training/data/meta/random.txt]]
+        [regions, [/workspaces/training/nf-training/data/meta/regions.json, /workspaces/training/nf-training/data/meta/regions.tsv, /workspaces/training/nf-training/data/meta/regions.yml]]
+        [regions2, [/workspaces/training/nf-training/data/meta/regions2.json]]
         ```
 
 ### `join()`
@@ -493,7 +493,7 @@ for (List row : lines) {
         Add a CSV text file containing the following, as an example input with the name "fastq.csv":
 
         ```csv title="fastq.csv"
-        gut,/workspace/gitpod/nf-training/data/ggal/gut_1.fq,/workspace/gitpod/nf-training/data/ggal/gut_2.fq
+        gut,/workspaces/training/nf-training/data/ggal/gut_1.fq,/workspaces/training/nf-training/data/ggal/gut_2.fq
         ```
 
         Then replace the input channel for the reads in `script7.nf`. Changing the following lines:

docs/basic_training/orientation.md

@@ -68,7 +68,7 @@ export NXF_VER=23.10.1
     Open the GitHub Codespaces training environment and use the following command to switch to the `nf-customize` folder. View the files in this folder using the `tree` command:
 
     ```bash
-    cd /workspace/gitpod/nf-training
+    cd /workspaces/training/nf-training
     tree .
     ```
 

docs/basic_training/orientation.pt.md

@@ -68,7 +68,7 @@ export NXF_VER=23.10.1
     Abra o [ambiente de treinamento no Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training) e use o seguinte comando para ir até a pasta `nf-customize`. Visualize os arquivos nessa pasta utilizando o comando `tree`:
 
     ```bash
-    cd /workspace/gitpod/nf-training
+    cd /workspaces/training/nf-training
     tree .
     ```
 

docs/basic_training/processes.md

@@ -171,7 +171,7 @@ workflow {
 Your expected output will look something like this:
 
 ```console title="Output"
-The current directory is /workspace/gitpod/nf-training/work/7a/4b050a6cdef4b6c1333ce29f7059a0
+The current directory is /workspaces/training/nf-training/work/7a/4b050a6cdef4b6c1333ce29f7059a0
 ```
 
 It can be tricky to write a script that uses many Bash variables. One possible alternative is to use a `script` string delimited by single-quote characters (`'`).
@@ -194,7 +194,7 @@ workflow {
 Your expected output will look something like this:
 
 ```console title="Output"
-The current directory is /workspace/gitpod/nf-training/work/7a/4b050a6cdef4b6c1333ce29f7059a0
+The current directory is /workspaces/training/nf-training/work/7a/4b050a6cdef4b6c1333ce29f7059a0
 ```
 
 However, using the single quotes (`'`) will block the usage of Nextflow variables in the command script.
@@ -753,7 +753,7 @@ workflow {
 Prints the following:
 
 ```console title="Output"
-[/workspace/gitpod/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_aa, /workspace/gitpod/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ab, /workspace/gitpod/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ac, /workspace/gitpod/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ad]
+[/workspaces/training/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_aa, /workspaces/training/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ab, /workspaces/training/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ac, /workspaces/training/nf-training/work/ca/baf931d379aa7fa37c570617cb06d1/chunk_ad]
 ```
 
 Some caveats on glob pattern behavior:
@@ -790,10 +790,10 @@ Some caveats on glob pattern behavior:
         Your output will look something like this:
 
         ```console title="Output"
-        /workspace/gitpod/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_aa
-        /workspace/gitpod/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ab
-        /workspace/gitpod/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ac
-        /workspace/gitpod/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ad
+        /workspaces/training/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_aa
+        /workspaces/training/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ab
+        /workspaces/training/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ac
+        /workspaces/training/nf-training/work/54/9d79f9149f15085e00dde2d8ead150/chunk_ad
         ```
 
 ### Dynamic output file names
@@ -861,9 +861,9 @@ workflow {
 The output will looks something like this:
 
 ```console title="Output"
-[lung, /workspace/gitpod/nf-training/work/23/fe268295bab990a40b95b7091530b6/sample.bam]
-[liver, /workspace/gitpod/nf-training/work/32/656b96a01a460f27fa207e85995ead/sample.bam]
-[gut, /workspace/gitpod/nf-training/work/ae/3cfc7cf0748a598c5e2da750b6bac6/sample.bam]
+[lung, /workspaces/training/nf-training/work/23/fe268295bab990a40b95b7091530b6/sample.bam]
+[liver, /workspaces/training/nf-training/work/32/656b96a01a460f27fa207e85995ead/sample.bam]
+[gut, /workspaces/training/nf-training/work/ae/3cfc7cf0748a598c5e2da750b6bac6/sample.bam]
 ```
 
 !!! question "Exercise"

docs/basic_training/rnaseq_pipeline.fr.md

@@ -42,7 +42,7 @@ nextflow run script1.nf
 Essayez de spécifier un paramètre d'entrée différent dans votre commande d'exécution, par exemple :
 
 ```bash
-nextflow run script1.nf --reads '/workspace/gitpod/nf-training/data/ggal/lung_{1,2}.fq'
+nextflow run script1.nf --reads '/workspaces/training/nf-training/data/ggal/lung_{1,2}.fq'
 ```
 
 ### :material-progress-question: Exercices
@@ -226,7 +226,7 @@ docker.enabled = true
         │       │   ├── refseq.bin
         │       │   ├── seq.bin
         │       │   └── versionInfo.json
-        │       └── transcriptome.fa -> /workspace/Gitpod_test/data/ggal/transcriptome.fa
+        │       └── transcriptome.fa -> /workspaces/training/data/ggal/transcriptome.fa
         ├── 7f
         ```