Fixed typos and updated license

LICENSE.txt

@@ -0,0 +1,19 @@
+Copyright (c) 2018, Centre for Genomic Regulation (CRG).
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

channel-duplication/README.md

@@ -6,8 +6,7 @@ You need to you use the same channel as input in two or more processes.
 
 ## Solution
 
-Use the [into](https://www.nextflow.io/docs/latest/operator.html#into) operator to create two (or more) copies of the source channel, 
-then use the new channels as the input of the processes. 
+Use the [into](https://www.nextflow.io/docs/latest/operator.html#into) operator to create two (or more) copies of the source channel. Then, use the new channels as input for the processes. 
 
 ## Code 
 
@@ -29,7 +28,7 @@ process bar {
   input: file x from prot2_ch
   script: 
   """
-    echo your_command --input $x
+    your_command --input $x
   """
 }    
 

channel-duplication/main.nf

@@ -1,24 +1,25 @@
 #!/usr/bin/env nextflow
 
 /*
+ * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
  *
- * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
- * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
- *
- *   This file is part of 'Nextflow'.
- *
- *   Nextflow is free software: you can redistribute it and/or modify
- *   it under the terms of the GNU General Public License as published by
- *   the Free Software Foundation, either version 3 of the License, or
- *   (at your option) any later version.
- *
- *   Nextflow is distributed in the hope that it will be useful,
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *   GNU General Public License for more details.
- *
- *   You should have received a copy of the GNU General Public License
- *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
  */
 
  /*

collect-into-file/README.md

@@ -1,13 +1,13 @@
-# Collect into a file 
+# Collect outputs into a file
 
 ## Problem 
 
-You need to concatenate into a single file all the outputs an upstream process. 
+You need to concatenate into a single file all output files produced by an upstream process. 
 
 ## Solution 
 
-Use the [https://www.nextflow.io/docs/latest/operator.html#collectfile] to merge all
-upstream output files into a single file. 
+Use the [collectFile](https://www.nextflow.io/docs/latest/operator.html#collectfile) operator to merge all
+the output files into a single file. 
 
 ## Code
 

collect-into-file/main.nf

@@ -1,23 +1,25 @@
 #!/usr/bin/env nextflo
 
 /*
- * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
- * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
+ * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
  *
- *   This file is part of 'Nextflow'.
- *
- *   Nextflow is free software: you can redistribute it and/or modify
- *   it under the terms of the GNU General Public License as published by
- *   the Free Software Foundation, either version 3 of the License, or
- *   (at your option) any later version.
- *
- *   Nextflow is distributed in the hope that it will be useful,
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *   GNU General Public License for more details.
- *
- *   You should have received a copy of the GNU General Public License
- *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
  */
 
  /*

conditional-process/README.md

@@ -8,10 +8,10 @@ then a third task should post-process the results of the previous execution.
 ## Solution
 
 Use a [when](https://www.nextflow.io/docs/latest/process.html#when) statement to conditionally 
-execute the two processes, having each of them to declare two different output channels.
+execute two different processes. Each process declares its own output channel.
 
-Then use the [mix](https://www.nextflow.io/docs/latest/operator.html#mix) to create 
-a new channel that holds the outputs produced by the two process and use it as the input
+Then use the [mix](https://www.nextflow.io/docs/latest/operator.html#mix) operator to create 
+a new channel that will emit the outputs produced by the two processes and use it as the input
 for the third process.
 
 ## Code 

conditional-process/main.nf

@@ -1,24 +1,25 @@
 #!/usr/bin/env nextflow
 
 /*
+ * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
  *
- * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
- * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
- *
- *   This file is part of 'Nextflow'.
- *
- *   Nextflow is free software: you can redistribute it and/or modify
- *   it under the terms of the GNU General Public License as published by
- *   the Free Software Foundation, either version 3 of the License, or
- *   (at your option) any later version.
- *
- *   Nextflow is distributed in the hope that it will be useful,
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *   GNU General Public License for more details.
- *
- *   You should have received a copy of the GNU General Public License
- *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
  */
 
  /*

feedback-loop/README.md

@@ -2,18 +2,16 @@
 
 ## Problem 
 
-Iterate the execution of one or more processes until  a condition
-is reached. 
+You need to repeat the execution of one or more tasks, using the output as the input for a new iteration, until a certain condition is reached. 
 
 ## Solution
 
-Use the output of the process to iterate over as the input of the same or an upstream process. 
+Use the output of the last process in the iteration loop as the input for the first process. 
 
-To do so, explicitly create the output channel using [Channel.create](https://www.nextflow.io/docs/latest/channel.html#create) function. 
+To do so, explicitly create the output channel using [Channel.create](https://www.nextflow.io/docs/latest/channel.html#create) method. 
 
-Then define the process input as a mix of of the initial input and the
-process output to which is applied an [until]() operator defining the 
-termination condition. 
+Then define the process input as a [mix](https://www.nextflow.io/docs/latest/operator.html#mix) of the initial input and the
+process output to which is applied the [until](https://www.nextflow.io/docs/latest/operator.html#until) operator which defines the termination condition. 
 
 ## Code 
 

feedback-loop/main.nf

@@ -1,24 +1,25 @@
 #!/usr/bin/env nextflow
 
 /*
+ * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
  *
- * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
- * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
- *
- *   This file is part of 'Nextflow'.
- *
- *   Nextflow is free software: you can redistribute it and/or modify
- *   it under the terms of the GNU General Public License as published by
- *   the Free Software Foundation, either version 3 of the License, or
- *   (at your option) any later version.
- *
- *   Nextflow is distributed in the hope that it will be useful,
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *   GNU General Public License for more details.
- *
- *   You should have received a copy of the GNU General Public License
- *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
  */
 
  /*

ignore-failing-process/README.md

@@ -2,12 +2,11 @@
 
 ## Problem 
 
-A process is expected to fail in certain situation. It's required to ignore
-the failing process and allows the remaining workflow to complete. 
+A task is expected to fail in a certain condition. You want to ignore the failure and continue the execution of the remaining tasks in the workflow. 
 
 ## Solution
 
-Use the `errorStrategy 'ignore'` [directive](https://www.nextflow.io/docs/latest/process.html#errorstrategy) to ignore the error condition. 
+Use the process [directive](https://www.nextflow.io/docs/latest/process.html#errorstrategy) `errorStrategy 'ignore'` to ignore the error condition. 
 
 
 ## Code 

ignore-failing-process/main.nf

@@ -1,24 +1,25 @@
 #!/usr/bin/env nextflow
 
 /*
+ * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
  *
- * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
- * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
- *
- *   This file is part of 'Nextflow'.
- *
- *   Nextflow is free software: you can redistribute it and/or modify
- *   it under the terms of the GNU General Public License as published by
- *   the Free Software Foundation, either version 3 of the License, or
- *   (at your option) any later version.
- *
- *   Nextflow is distributed in the hope that it will be useful,
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *   GNU General Public License for more details.
- *
- *   You should have received a copy of the GNU General Public License
- *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
  */
 
  /*

optional-input/README.md

@@ -6,7 +6,30 @@ One or more processes have an optional input file.
 
 ## Solution 
 
-Use a mock file name to simulate the absence of the file parameter. 
+Use a special file name to mark the absence of the file parameter. 
+
+## Code 
+
+```nextflow
+
+params.inputs = 'prots/*{1,2,3}.fa'
+params.filter = 'NO_FILE'
+
+prots_ch = Channel.fromPath(params.inputs)
+opt_file = file(params.filter)
+
+process foo {
+  input:
+  file seq from prots_ch
+  file opt from opt_file 
+
+  script:
+  def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
+  """
+  your_commad --input $seq $filter
+  """
+}
+```
 
 ## Run it