add newlines after pictures.

2_functional_metagenomic_profiling/2_demo_ngless/ngless.Rmd

@@ -249,6 +249,7 @@ dataset:
 
 ![](./pictures/pic_1.png)
 
+
 The file `ngless_pipeline.ngl` contains the example script that we have seen
 in the section above. The output folder is present, since we want to save our 
 results in this folder (see in the script).
@@ -257,10 +258,12 @@ The file `toy_samples` contains a list of metagenomes we want to analyse:
 
 ![](./pictures/pic_3.png)
 
+
 The sample folders contain the actual sequencing reads:
 
 ![](./pictures/pic_2.png)
 
+
 I have create my own conda environment for `NGLess`, so I will first activate
 this:
 
@@ -282,16 +285,19 @@ you which references should be cited:
 
 ![](./pictures/pic_4.png)
 
+
 During the run, `NGLess` will print some basic information about the analysis
 on the screen:
 
 ![](./pictures/pic_5_1.png)
 ![](./pictures/pic_5_2.png)
 
+
 Now, the `NGLess` run has finished. How does our example folder look like now?
 
 ![](./pictures/pic_6.png)
 
+
 As you can see, `NGLess` has create a few folders in which it saves some 
 temporary results. Those are:
 
@@ -304,6 +310,7 @@ by `NGLess`. Samples can either be locked, finished, or failed.
 
 ![](./pictures/pic_7.png)
 
+
 The partials folder contains the partial results. In our case, there is one
 folder for the IGC mappings...
 
@@ -329,6 +336,7 @@ After we have done so, we should see one finished lock for each sample:
 
 ![](./pictures/pic_11.png)
 
+
 and the results in the `output` folder:
 
 ![](./pictures/pic_12.png)

2_functional_metagenomic_profiling/2_demo_ngless/ngless.md

@@ -249,6 +249,7 @@ dataset:
 
 ![](./pictures/pic_1.png)
 
+
 The file `ngless_pipeline.ngl` contains the example script that we have seen
 in the section above. The output folder is present, since we want to save our 
 results in this folder (see in the script).
@@ -257,10 +258,12 @@ The file `toy_samples` contains a list of metagenomes we want to analyse:
 
 ![](./pictures/pic_3.png)
 
+
 The sample folders contain the actual sequencing reads:
 
 ![](./pictures/pic_2.png)
 
+
 I have create my own conda environment for `NGLess`, so I will first activate
 this:
 
@@ -282,16 +285,19 @@ you which references should be cited:
 
 ![](./pictures/pic_4.png)
 
+
 During the run, `NGLess` will print some basic information about the analysis
 on the screen:
 
 ![](./pictures/pic_5_1.png)
 ![](./pictures/pic_5_2.png)
 
+
 Now, the `NGLess` run has finished. How does our example folder look like now?
 
 ![](./pictures/pic_6.png)
 
+
 As you can see, `NGLess` has create a few folders in which it saves some 
 temporary results. Those are:
 
@@ -304,6 +310,7 @@ by `NGLess`. Samples can either be locked, finished, or failed.
 
 ![](./pictures/pic_7.png)
 
+
 The partials folder contains the partial results. In our case, there is one
 folder for the IGC mappings...
 
@@ -329,6 +336,7 @@ After we have done so, we should see one finished lock for each sample:
 
 ![](./pictures/pic_11.png)
 
+
 and the results in the `output` folder:
 
 ![](./pictures/pic_12.png)