Troubleshooting Edits

Mention Nextflow config repository, and solution for VCF files with non-standard chromosomes

docs/troubleshooting.rst

@@ -17,7 +17,11 @@ The workflow isn't using many resources (e.g. RAM / CPU)
 
 Did you forget to set ``--max_cpu`` or ``--max_memory?``
 
-You can also edit ``nextflow.config`` to configure cpu and memory permanently.
+You can also edit ``nextflow.config`` to configure cpu and memory permanently. nf-core
+provides a `set of example .config files`_, including examples for both institutional
+compute clusters (e.g. Cambridge, Sanger) and cloud compute providers (e.g. Google, AWS Tower and Batch).
+
+.. _set of example .config files : https://github.com/nf-core/configs
 
 When I run the workflow I get an error about software not being installed
 -------------------------------------------------------------------------
@@ -37,6 +41,16 @@ it. Here's a simple method to do this (`thanks to Rvtests`_):
 
 .. code-block:: console
 
-    (zgrep ^"#" $your_old_vcf; zgrep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file.gz 
+    (zgrep ^"#" $your_old_vcf; zgrep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file.gz
+
+VCF file(s) containing variants on non-standard chromsomes or patches (e.g. chr1_gl000191_random) will also currently fail
+our pipeline as it only takes human chromosomes as input (1-22, X, Y, XY). One way to remove these variants is to download
+and run plink2 and convert your data to plink files that can be used with the calculator using the following command:
+
+.. code-block:: console
+
+    plink2 --vcf [yourfile] --allow-extra-chr --chr 1-22, X, Y, XY -make-pgen --out [yourfile]_axy
+
+however other methods to filter these variants from VCFs also exist.
 
 .. _`thanks to Rvtests`: http://zhanxw.github.io/rvtests/#input-files