Merge branch 'smw-tb-vcf-dev' into smw-tb-2023-10-25-dev

theiagen · Oct 25, 2023 · c6fac1e · c6fac1e
2 parents ba8d60d + 0251379
commit c6fac1e
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Showing 5 changed files with 10 additions and 4 deletions.
diff --git a/tasks/species_typing/task_tbprofiler.wdl b/tasks/species_typing/task_tbprofiler.wdl
@@ -42,7 +42,6 @@ task tbprofiler {
 
     # check if new database file is provided and not empty
     if [ "~{tbprofiler_run_custom_db}" = true ] ; then
-
       echo "Found new database file ~{tbprofiler_custom_db}"
       prefix=$(basename "~{tbprofiler_custom_db}" | sed 's/\.tar\.gz$//')
       echo "New database will be created with prefix $prefix"
@@ -53,11 +52,8 @@ task tbprofiler {
       tb-profiler load_library ./"$prefix"/"$prefix"
 
       TBDB="--db $prefix"
-
     else
-
       TBDB=""
-
     fi
 
     # Run tb-profiler on the input reads with samplename prefix
@@ -81,6 +77,11 @@ task tbprofiler {
     # touch optional output files because wdl
     touch GENE_NAME LOCUS_TAG VARIANT_SUBSTITUTIONS OUTPUT_SEQ_METHOD_TYPE
 
+    # merge all vcf files if multiple are present
+    bcftools index ./vcf/*bcf
+    bcftools index ./vcf/*gz
+    bcftools merge --force-samples ./vcf/*bcf ./vcf/*gz > ./vcf/~{samplename}.targets.csq.merged.vcf
+
     python3 <<CODE
     import csv
     import json
@@ -127,6 +128,7 @@ task tbprofiler {
     File tbprofiler_output_json = "./results/~{samplename}.results.json"
     File tbprofiler_output_bam = "./bam/~{samplename}.bam"
     File tbprofiler_output_bai = "./bam/~{samplename}.bam.bai"
+    File tbprofiler_output_vcf = "./vcf/~{samplename}.targets.csq.merged.vcf"
     String version = read_string("VERSION")
     String tbprofiler_main_lineage = read_string("MAIN_LINEAGE")
     String tbprofiler_sub_lineage = read_string("SUB_LINEAGE")

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
@@ -818,6 +818,7 @@ workflow theiaprok_illumina_pe {
     File? tbprofiler_output_file = merlin_magic.tbprofiler_output_file
     File? tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam
     File? tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai
+    File? tbprofiler_output_vcf = merlin_magic.tbprofiler_output_vcf
     String? tbprofiler_version = merlin_magic.tbprofiler_version
     String? tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage
     String? tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -770,6 +770,7 @@ workflow theiaprok_illumina_se {
     File? tbprofiler_output_file = merlin_magic.tbprofiler_output_file
     File? tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam
     File? tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai
+    File? tbprofiler_output_vcf = merlin_magic.tbprofiler_output_vcf
     String? tbprofiler_version = merlin_magic.tbprofiler_version
     String? tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage
     String? tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage

diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl
@@ -732,6 +732,7 @@ workflow theiaprok_ont {
     File? tbprofiler_output_file = merlin_magic.tbprofiler_output_file
     File? tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam
     File? tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai
+    File? tbprofiler_output_vcf = merlin_magic.tbprofiler_output_vcf
     String? tbprofiler_version = merlin_magic.tbprofiler_version
     String? tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage
     String? tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage

diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
@@ -580,6 +580,7 @@ workflow merlin_magic {
     File? tbprofiler_output_file = tbprofiler.tbprofiler_output_csv
     File? tbprofiler_output_bam = tbprofiler.tbprofiler_output_bam
     File? tbprofiler_output_bai = tbprofiler.tbprofiler_output_bai
+    File? tbprofiler_output_vcf = tbprofiler.tbprofiler_output_vcf
     String? tbprofiler_version = tbprofiler.version
     String? tbprofiler_main_lineage = tbprofiler.tbprofiler_main_lineage
     String? tbprofiler_sub_lineage = tbprofiler.tbprofiler_sub_lineage