Merge branch 'dev' into saltshaker

Author: ramprasadn

subworkflows/local/align/tests/main.nf.test

@@ -3,8 +3,17 @@ nextflow_workflow {
     name "Test Workflow ALIGN"
     script "subworkflows/local/align/main.nf"
     workflow "ALIGN"
+
     tag "subworkflows"
     tag "align"
+    tag "align_bwa_bwamem2_bwameme"
+    tag "align_sentieon"
+    tag "align_MT"
+    tag "convert_mt_bam_to_fastq"
+
+    tag "fastp"
+    tag "samtools/view"
+
     config "./nextflow.config"
 
     setup {

subworkflows/local/align_MT/tests/main.nf.test

@@ -3,8 +3,18 @@ nextflow_workflow {
     name "Test Workflow ALIGN_MT"
     script "subworkflows/local/align_MT/main.nf"
     workflow "ALIGN_MT"
+
     tag "subworkflows"
     tag "align_mt"
+
+    tag "bwa/mem"
+    tag "bwamem2/mem"
+    tag "sentieon/bwamem"
+    tag "gatk4/mergebamalignment"
+    tag "picard/addorreplacereadgroups"
+    tag "picard/markduplicates"
+    tag "samtools/sort"
+
     config "./nextflow.config"
 
     test("align mt - bwamem2") {

subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test

@@ -3,8 +3,19 @@ nextflow_workflow {
     name "Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME"
     script "subworkflows/local/align_bwa_bwamem2_bwameme/main.nf"
     workflow "ALIGN_BWA_BWAMEM2_BWAMEME"
+
     tag "subworkflows"
     tag "align_bwa_bwamem2_bwameme"
+
+    tag "bwa/mem"
+    tag "bwamem2/mem"
+    tag "bwameme/mem"
+    tag "samtools/index"
+    tag "samtools/stats"
+    tag "samtools/merge"
+    tag "samtools/view"
+    tag "picard/markduplicates"
+
     config "./nextflow.config"
 
     test("align bwamem2") {

subworkflows/local/align_sentieon/tests/main.nf.test

@@ -3,8 +3,16 @@ nextflow_workflow {
     name "Test Workflow ALIGN_SENTIEON"
     script "subworkflows/local/align_sentieon/main.nf"
     workflow "ALIGN_SENTIEON"
+
     tag "subworkflows"
     tag "align_sentieon"
+
+    tag "sentieon/bwamem"
+    tag "sentieon/datametrics"
+    tag "sentieon/dedup"
+    tag "sentieon/readwriter"
+    tag "samtools/view"
+
     config "./nextflow.config"
 
     test("align sentieon") {

subworkflows/local/annotate_cadd/tests/main.nf.test

@@ -3,8 +3,16 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_CADD"
     script "subworkflows/local/annotate_cadd/main.nf"
     workflow "ANNOTATE_CADD"
+
     tag "subworkflows"
     tag "annotate_cadd"
+
+    tag "bcftools/annotate"
+    tag "bcftools/view"
+    tag "cadd"
+    tag "gawk"
+    tag "tabix/tabix"
+
     config "./nextflow.config"
 
     test("ANNOTATE_CADD - GRCh37, stub") {

subworkflows/local/annotate_consequence_pli/tests/main.nf.test

@@ -3,6 +3,11 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_CSQ_PLI"
     script "subworkflows/local/annotate_consequence_pli/main.nf"
     workflow "ANNOTATE_CSQ_PLI"
+
+    tag "custom/addmostsevereconsequence"
+    tag "custom/addmostseverepli"
+    tag "tabix/tabix"
+
     tag "subworkflows"
     tag "annotate_consequence_pli"
 

subworkflows/local/annotate_genome_snvs/tests/main.nf.test

@@ -3,8 +3,23 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_GENOME_SNVS"
     script "subworkflows/local/annotate_genome_snvs/main.nf"
     workflow "ANNOTATE_GENOME_SNVS"
+
     tag "subworkflows"
     tag "annotate_genome_snvs"
+    tag "annotate_cadd"
+    tag "annotate_rhocallviz"
+
+    tag "vcfanno"
+    tag "bcftools/concat"
+    tag "bcftools/roh"
+    tag "bcftools/view"
+    tag "rhocall/annotate"
+    tag "upd"
+    tag "chromograph"
+    tag "ensemblvep/vep"
+    tag "tabix/bgziptabix"
+    tag "gatk4/selectvariants"
+
     config "./nextflow.config"
 
     test("ANNOTATE_GENOME_SNVS - GRCh37, stub") {

subworkflows/local/annotate_mobile_elements/tests/main.nf.test

@@ -3,8 +3,15 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_MOBILE_ELEMENTS"
     script "subworkflows/local/annotate_mobile_elements/main.nf"
     workflow "ANNOTATE_MOBILE_ELEMENTS"
+
     tag "subworkflows"
     tag "annotate_mobile_elements"
+
+    tag "bcftools/view"
+    tag "ensemblvep/vep"
+    tag "picard/sortvcf"
+    tag "svdb/query"
+
     config "./nextflow.config"
 
     test("ANNOTATE_MOBILE_ELEMENTS - GRCh37, stub") {

subworkflows/local/annotate_mt_snvs/tests/main.nf.test

@@ -3,8 +3,18 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_MT_SNVS"
     script "subworkflows/local/annotate_mt_snvs/main.nf"
     workflow "ANNOTATE_MT_SNVS"
+
     tag "subworkflows"
     tag "annotate_mt_snvs"
+    tag "annotate_cadd"
+
+    tag "bcftools/pluginsetgt"
+    tag "tabix/tabix"
+    tag "ensemblvep/vep"
+    tag "haplogrep3/classify"
+    tag "vcfanno"
+    tag "tabix/bgziptabix"
+
     config "./nextflow.config"
 
     test("ANNOTATE_MT_SNVS - GRCh37, stub") {

subworkflows/local/annotate_rhocallviz/tests/main.nf.test

@@ -3,8 +3,16 @@ nextflow_workflow {
     name "Test Workflow ANNOTATE_RHOCALLVIZ"
     script "subworkflows/local/annotate_rhocallviz/main.nf"
     workflow "ANNOTATE_RHOCALLVIZ"
+
     tag "subworkflows"
     tag "annotate_rhocallviz"
+
+    tag "bcftools/view"
+    tag "bcftools/roh"
+    tag "rhocall/viz"
+    tag "ucsc/wigtobigwig"
+    tag "chromograph"
+
     config "./nextflow.config"
 
     test("ANNOTATE_RHOCALLVIZ - stub") {