Add subworkflows

.gitpod.yml

@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code

bin/concatenateVCFs.sh

@@ -59,7 +59,7 @@ then
 
     CONTIGS=($(cut -f1 ${genomeIndex}))
 
-    # Concatenate VCFs in the correct order
+    #Concatenate VCFs in the correct order
     (
         cat header
 
@@ -68,7 +68,7 @@ then
             # "ls: cannot access chr3_*.vcf: No such file or directory" when chr3
             # was not processed.
             pattern="${chr}_*.vcf"
-            if ! compgen -G "${pattern}" > /dev/null; then continue; fi
+            if ! compgen -G "${pattern}" > /dev/null ; then continue; fi
 
             # ls -v sorts by numeric value ("version"), which means that chr1_100_
             # is sorted *after* chr1_99_.

conf/genomes.config

@@ -29,15 +29,6 @@ params {
             fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
             known_indels          = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
         }
-        'smallGRCh38' {
-            dbsnp                 = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz"
-            fasta                 = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta"
-            known_indels          = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz"
-            snpeff_db             = 'GRCh38.99'
-            vep_genome            = 'GRCh38'
-            vep_species           = 'homo_sapiens'
-            vep_cache_version     = '99'
-        }
         'custom' {
             fasta                 = null
         }