Update docs + some fix

README.md

@@ -91,6 +91,7 @@ Helpful contributors:
 * [James A. Fellows Yates](https://github.com/jfy133)
 * [Jesper Eisfeldt](https://github.com/J35P312)
 * [Johannes Alneberg](https://github.com/alneberg)
+* [José Fernández Navarro](https://github.com/jfnavarro)
 * [Lucia Conde](https://github.com/lconde-ucl)
 * [Malin Larsson](https://github.com/malinlarsson)
 * [Marcel Martin](https://github.com/marcelm)

docs/usage.md

@@ -120,7 +120,7 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.
 
-Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config:
+Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `VEP` 32GB of memory, you could use the following config:
 
 ```nextflow
 process {
@@ -130,6 +130,16 @@ process {
 }
 ```
 
+Alternatively, to give the workflow both processes `VEP` and `VEPmerge` 32GB of memory, you could use the following config:
+
+```nextflow
+process {
+  withLabel: VEP {
+    memory = 32.GB
+  }
+}
+```
+
 See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.
 
 If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition above). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

main.nf

@@ -3417,11 +3417,8 @@ process ControlFreecViz {
 
     script:
     """
-    echo "Shaping CNV files to make sure we can assess significance"
-    LINEWIDTH=`head -1 ${cnvTumor}| wc -w`; awk 'NF=='$LINEWIDTH'{print}' ${cnvTumor} > TUMOR.CNVs
-
     echo "############### Calculating significance values for TUMOR CNVs #############"
-    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args TUMOR.CNVs ${ratioTumor}
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvtumor} ${ratioTumor}
 
     echo "############### Creating graph for TUMOR ratios ###############"
     cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
@@ -3450,11 +3447,8 @@ process ControlFreecVizSingle {
 
     script:
     """
-    echo "Shaping CNV files to make sure we can assess significance"
-    LINEWIDTH=`head -1 ${cnvTumor}| wc -w`; awk 'NF=='$LINEWIDTH'{print}' ${cnvTumor} > TUMOR.CNVs
-
     echo "############### Calculating significance values for TUMOR CNVs #############"
-    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args TUMOR.CNVs ${ratioTumor}
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvtumor} ${ratioTumor}
 
     echo "############### Creating graph for TUMOR ratios ###############"
     cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}