Convert to mkdocs

.github/workflows/deploy.yml

@@ -0,0 +1,15 @@
+name: deploy
+on:
+  push:
+    branches:
+      - master
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material
+      - run: mkdocs gh-deploy --force

.github/workflows/test.yml

@@ -0,0 +1,13 @@
+name: test
+on: push
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+      - uses: nf-core/setup-nextflow@v1
+      - run: bash scripts/test.sh

.gitignore

@@ -1,6 +1,7 @@
-.git/
-.nextflow*
+.git
 .idea*
-work/
+.nextflow*
+my-results
+public
 results
-my-results
+work

README.md

@@ -2,46 +2,46 @@
 
 A curated collection of Nextflow implementation patterns  
 
-[![Build Status](https://travis-ci.org/nextflow-io/patterns.svg?branch=master)](https://travis-ci.org/nextflow-io/patterns)
+![Build Status](https://github.com/nextflow-io/patterns/actions/workflows/test.yml/badge.svg)
 
 ## Basic patterns
 
-* [Channel duplication](docs/channel-duplication.adoc)
+* [Channel duplication](docs/channel-duplication.md)
 
-### Scatter executions
+## Scatter executions
 
-* [Process per file path](docs/process-per-file-path.adoc)
-* [Process per file chunk](docs/process-per-file-chunk.adoc)
-* [Process per file pairs](docs/process-per-file-pairs.adoc)
-* [Process per file range](docs/process-per-file-range.adoc)
-* [Process per CSV record](docs/process-per-csv-record.adoc)
-* [Process per file output](docs/process-per-file-output.adoc)
+* [Process per file path](docs/process-per-file-path.md)
+* [Process per file chunk](docs/process-per-file-chunk.md)
+* [Process per file pairs](docs/process-per-file-pairs.md)
+* [Process per file range](docs/process-per-file-range.md)
+* [Process per CSV record](docs/process-per-csv-record.md)
+* [Process per file output](docs/process-per-file-output.md)
 
-### Gather results
+## Gather results
 
-* [Process all outputs altogether](docs/process-collect.adoc)
-* [Process outputs into groups](docs/process-into-groups.adoc)
-* [Collect outputs into a file](docs/collect-into-file.adoc)
+* [Process all outputs altogether](docs/process-collect.md)
+* [Process outputs into groups](docs/process-into-groups.md)
+* [Collect outputs into a file](docs/collect-into-file.md)
 
-### Organize outputs
+## Organize outputs
 
-* [Store process outputs](docs/publish-process-outputs.adoc)
-* [Store outputs matching a glob pattern](docs/publish-matching-glob.adoc)
-* [Store outputs renaming files](docs/publish-rename-outputs.adoc)
+* [Store process outputs](docs/publish-process-outputs.md)
+* [Store outputs matching a glob pattern](docs/publish-matching-glob.md)
+* [Store outputs renaming files](docs/publish-rename-outputs.md)
 
 ## Other
 
-* [Get process work directory](docs/process-get-workdir.adoc)
-* [Ignore failing process](docs/ignore-failing-process.adoc)
-* [State dependency](docs/state-dependency.adoc)
+* [Get process work directory](docs/process-get-workdir.md)
+* [Ignore failing process](docs/ignore-failing-process.md)
+* [State dependency](docs/state-dependency.md)
 
 ## Advanced patterns
 
-* [Conditional process resources](docs/conditional-resources.adoc)
-* [Conditional process executions](docs/conditional-process.adoc)
-* [Skip process execution](docs/skip-process-execution.adoc)
-* [Feedback loop](docs/feedback-loop.adoc)
-* [Optional input](docs/optional-input.adoc)
-* [Optional output](docs/optional-output.adoc)
-* [Process when empty](docs/process-when-empty.adoc)
-* [Task batching](docs/task-batching.adoc)
+* [Conditional process resources](docs/conditional-resources.md)
+* [Conditional process executions](docs/conditional-process.md)
+* [Skip process execution](docs/skip-process-execution.md)
+* [Feedback loop](docs/feedback-loop.md)
+* [Optional input](docs/optional-input.md)
+* [Optional output](docs/optional-output.md)
+* [Process when empty](docs/process-when-empty.md)
+* [Task batching](docs/task-batching.md)

docs/channel-duplication.adoc → docs/channel-duplication.md

@@ -1,17 +1,14 @@
-= Channel duplication   
-
-== Problem 
+## Problem 
 
 You need to you use the same channel as input in two or more processes.
 
-== Solution
+## Solution
 
-In DSL2, you can just do it! The https://www.nextflow.io/docs/latest/operator.html#into[into] operator is no longer needed.
+In DSL2, you can just do it! The [into](https://www.nextflow.io/docs/latest/operator.html#into) operator is no longer needed.
 
-== Code 
+## Code 
 
-[source,nextflow,linenums,options="nowrap"]
-----
+```groovy
 process foo {
   input: path x
   script: 
@@ -34,12 +31,12 @@ workflow {
   foo(input_ch)
   bar(input_ch)
 }
-----
+```
 
-== Run it
+## Run it
 
 Use the the following command to execute the example:
 
-```
+```bash
 nextflow run patterns/channel-duplication.nf
 ```

docs/collect-into-file.adoc → docs/collect-into-file.md

@@ -1,18 +1,15 @@
-= Collect outputs into a file
-
-== Problem 
+## Problem 
 
 You need to concatenate into a single file all output files produced by an upstream process. 
 
-== Solution 
+## Solution 
 
-Use the https://www.nextflow.io/docs/latest/operator.html#collectfile[collectFile] operator to merge all
+Use the [collectFile](https://www.nextflow.io/docs/latest/operator.html#collectfile) operator to merge all
 the output files into a single file. 
 
-== Code
+## Code
 
-[source,nextflow,linenums,options="nowrap"]
-----
+```groovy
 process foo {
   input:
   path x
@@ -30,12 +27,12 @@ workflow {
     | collectFile \
     | view
 }
-----
+```
 
-== Run it
+## Run it
 
 Use the the following command to execute the example:
 
-```
+```bash
 nextflow run patterns/collect-into-file.nf
 ```

docs/conditional-process.adoc → docs/conditional-process.md

@@ -1,22 +1,19 @@
-= Conditional process executions 
-
-== Problem 
+## Problem 
 
 One of two different tasks should be executed based on some condition, 
 and a third task should process the results of the selected task.
 
-== Solution
+## Solution
 
 Simply execute either process using `if/else` statements on the condition.
 Define a channel, e.g. `omega_ch`, which emits the output of the selected process 
 in each case. Then, execute the third process with this output channel.
 
 Or, use a ternary expression and a pipe to keep things short and sweet.
 
-== Code 
+## Code 
 
-[source,nextflow,linenums,options="nowrap"]
-----
+```groovy
 params.flag = false 
 
 process foo {
@@ -66,39 +63,38 @@ workflow {
   // the short way
   (params.flag ? bar : foo) | omega
 }
-----
+```
 
-== Run it
+## Run it
 
 Use the the following command to execute the example:
 
-```
+```bash
 nextflow run patterns/conditional-process.nf
 ```
 
 The processes `foo` and `omega` are executed. Run the same command 
 with the `--flag` command line option. 
 
-```
+```bash
 nextflow run patterns/conditional-process.nf --flag 
 ```
 
 This time the processes `bar` and `omega` are executed.
 
-== Alternative solution
+## Alternative solution
 
 Create an input channel for each process that is either populated with data or an
-https://www.nextflow.io/docs/latest/channel.html#empty[empty] channel.
+[empty](https://www.nextflow.io/docs/latest/channel.html#empty) channel.
 Each process will execute only if its input channel has data.
 
-Then use the https://www.nextflow.io/docs/latest/operator.html#mix[mix] operator to create 
+Then use the [mix](https://www.nextflow.io/docs/latest/operator.html#mix) operator to create 
 a new channel that emits the outputs produced by the two processes, and use it as the input
 for the third process.
 
-== Code 
+## Code 
 
-[source,nextflow,linenums,options="nowrap"]
-----
+```groovy
 params.flag = false
 
 process foo {
@@ -148,10 +144,10 @@ workflow {
 
   foo.out | mix(bar.out) | omega
 }
-----
+```
 
-== Run it 
+## Run it 
 
-```
+```bash
 nextflow run patterns/conditional-process2.nf
 ```

docs/conditional-resources.adoc → docs/conditional-resources.md

@@ -1,12 +1,10 @@
-= Conditional resources definition 
-
-== Problem 
+## Problem 
 
 A task in your workflow needs to use some amount of computing 
 resources (e.g. memory) that depends on the size or the name of one 
 or more input files. 
 
-== Solution 
+## Solution 
 
 Declare the resource requirements (`memory`, `cpus`, etc.)
 in a dynamic manner using a closure. 
@@ -15,10 +13,9 @@ The closure computes the required amount of resources using the file
 attributes (e.g. `size`) of the inputs declared in the process
 definition.
 
-== Code 
+## Code 
 
-[source,nextflow,linenums,options="nowrap"]
-----
+```groovy
 process foo {
     memory { reads.size() < 70.KB ? 1.GB : 5.GB }
 
@@ -34,10 +31,10 @@ workflow {
     Channel.fromPath("$baseDir/data/reads/*_1.fq.gz", checkIfExists:true) \
         | foo
 }
-----
+```
 
-== Run it 
+## Run it 
 
-```
+```bash
 nextflow run patterns/conditional-resources.nf
 ```