diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
new file mode 100644
index 00000000..adcbd10f
--- /dev/null
+++ b/.github/CODEOWNERS
@@ -0,0 +1,4 @@
+# Test CODEOWNERS
+# Default owner(s)
+*	@tyamaguchi-ucla @yashpatel6 @maotian06 @sorelfitzgibbon @uclahs-cds/nextflow-wg
+# Folder specific owner
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e388bef2..da2c971f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- Add .github/CODEOWNERS
 - Add check for MuSE or Mutect2 on F2 node
 
 ### Changed
+- Reorder all VCFs before intersection
+- Move `filter_VCF_BCFtools` to `common.nf`
 - Fix blarchive compression log output directory
 - Delay readcount compression until original file is no longer needed
 
diff --git a/main.nf b/main.nf
index 5444bec7..44df748f 100755
--- a/main.nf
+++ b/main.nf
@@ -174,10 +174,10 @@ workflow {
         }
 
     // Set empty channels so any unused tools don't cause failure at intersect step
-    Channel.empty().set { somaticsniper_vcf_ch }
-    Channel.empty().set { strelka2_vcf_ch }
-    Channel.empty().set { mutect2_vcf_ch }
-    Channel.empty().set { muse_vcf_ch }
+    Channel.empty().set { somaticsniper_gzvcf_ch }
+    Channel.empty().set { strelka2_gzvcf_ch }
+    Channel.empty().set { mutect2_gzvcf_ch }
+    Channel.empty().set { muse_gzvcf_ch }
 
     Channel.empty().set { somaticsniper_idx_ch }
     Channel.empty().set { strelka2_idx_ch }
@@ -193,7 +193,7 @@ workflow {
             run_GetSampleName_Mutect2_normal.out.name_ch,
             run_GetSampleName_Mutect2_tumor.out.name_ch
             )
-            somaticsniper.out.vcf.set { somaticsniper_vcf_ch }
+            somaticsniper.out.gzvcf.set { somaticsniper_gzvcf_ch }
             somaticsniper.out.idx.set { somaticsniper_idx_ch }
         }
     if ('strelka2' in params.algorithm) {
@@ -205,7 +205,7 @@ workflow {
             run_GetSampleName_Mutect2_normal.out.name_ch,
             run_GetSampleName_Mutect2_tumor.out.name_ch
             )
-            strelka2.out.vcf.set { strelka2_vcf_ch }
+            strelka2.out.gzvcf.set { strelka2_gzvcf_ch }
             strelka2.out.idx.set { strelka2_idx_ch }
         }
     if ('mutect2' in params.algorithm) {
@@ -216,7 +216,7 @@ workflow {
             normal_input.normal_index.collect(),
             tumor_input.contamination_est.collect()
             )
-            mutect2.out.vcf.set { mutect2_vcf_ch }
+            mutect2.out.gzvcf.set { mutect2_gzvcf_ch }
             mutect2.out.idx.set { mutect2_idx_ch }
         }
     if ('muse' in params.algorithm) {
@@ -228,30 +228,28 @@ workflow {
             run_GetSampleName_Mutect2_normal.out.name_ch,
             run_GetSampleName_Mutect2_tumor.out.name_ch
             )
-            muse.out.vcf.set { muse_vcf_ch }
+            muse.out.gzvcf.set { muse_gzvcf_ch }
             muse.out.idx.set { muse_idx_ch }
         }
 
     // Intersect all vcf files
     if (params.algorithm.size() > 1) {
-        tool_vcfs = (somaticsniper_vcf_ch
-            .mix(strelka2_vcf_ch)
-            .mix(mutect2_vcf_ch)
-            .mix(muse_vcf_ch))
+        tool_gzvcfs = (somaticsniper_gzvcf_ch
+            .mix(strelka2_gzvcf_ch)
+            .mix(mutect2_gzvcf_ch)
+            .mix(muse_gzvcf_ch))
             .collect()
-
         tool_indices = (somaticsniper_idx_ch
             .mix(strelka2_idx_ch)
             .mix(mutect2_idx_ch)
             .mix(muse_idx_ch))
             .collect()
-
         intersect(
-            tool_vcfs,
+            tool_gzvcfs,
             tool_indices,
             script_dir_ch,
-            run_GetSampleName_Mutect2_normal.out.name_ch,
-            run_GetSampleName_Mutect2_tumor.out.name_ch
+            run_GetSampleName_Mutect2_normal.out.name_ch.first(),
+            run_GetSampleName_Mutect2_tumor.out.name_ch.first()
             )
         }
     }
diff --git a/module/common.nf b/module/common.nf
index a63ca7d2..4534fe6e 100644
--- a/module/common.nf
+++ b/module/common.nf
@@ -8,6 +8,31 @@ Docker Images:
 - docker_image_blarchive: ${params.docker_image_blarchive}
 """
 
+process filter_VCF_BCFtools {
+    container params.docker_image_BCFtools
+    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
+        mode: "copy",
+        pattern: "*.vcf.gz",
+        enabled: params.save_intermediate_files
+    publishDir path: "${params.workflow_log_output_dir}",
+        mode: "copy",
+        pattern: ".command.*",
+        saveAs: { "${task.process.split(':')[-1]}-${var_type}/log${file(it).getName()}" }
+
+    input:
+    tuple val(var_type), path(vcf)
+
+    output:
+    tuple val(var_type), path("*.vcf.gz"), emit: gzvcf
+    path ".command.*"
+
+    script:
+    """
+    set -euo pipefail
+    bcftools view -f PASS  --output-type z --output ${params.output_filename}_${var_type}-pass.vcf.gz ${vcf}
+    """
+    }
+
 process generate_sha512sum {
     container params.docker_image_validate_params
     publishDir path: "${params.workflow_output_dir}/output",
@@ -52,7 +77,7 @@ process rename_samples_BCFtools {
     tuple val(var_type), path(vcf)
 
     output:
-    tuple val(var_type), path("*.vcf.gz"), emit: fix_vcf
+    tuple val(var_type), path("*.vcf.gz"), emit: gzvcf
     path ".command.*"
     path "*_samples.txt"
 
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 6fac58de..d2e84f2b 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -10,6 +10,36 @@ Intersect Options:
 - vcf2maf_extra_args:  ${params.vcf2maf_extra_args}
 ====================================
 """
+process reorder_samples_BCFtools {
+    container params.docker_image_BCFtools
+    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
+        mode: "copy",
+        pattern: "*.vcf.gz",
+        enabled: params.save_intermediate_files
+    publishDir path: "${params.workflow_log_output_dir}",
+        mode: "copy",
+        pattern: ".command.*",
+        saveAs: { "${task.process.split(':')[-1]}-${algorithm}/log${file(it).getName()}" }
+
+    input:
+    tuple val(algorithm), path(gzvcf)
+    path indices
+    val tumor_id
+    val normal_id
+
+    output:
+    path "*-reorder.vcf.gz", emit: gzvcf
+    path ".command.*"
+
+    script:
+    """
+    set -euo pipefail
+    infile=\$(basename ${gzvcf} .vcf.gz)
+    outfile="\${infile}-reorder.vcf.gz"
+    bcftools view -s ${tumor_id},${normal_id} --output \${outfile} ${gzvcf}
+    """
+    }
+
 process intersect_VCFs_BCFtools {
     container params.docker_image_BCFtools
     publishDir path: "${params.workflow_output_dir}/output",
@@ -29,20 +59,20 @@ process intersect_VCFs_BCFtools {
         saveAs: { "${task.process.split(':')[-1]}/log${file(it).getName()}" }
 
     input:
-    path vcfs
+    path gzvcf
     path indices
     path intersect_regions
     path intersect_regions_index
 
     output:
-    path "*.vcf.gz", emit: intersect_vcf
-    path "*.vcf.gz.tbi", emit: intersect_idx
+    path "*.vcf.gz", emit: gzvcf
+    path "*.vcf.gz.tbi", emit: idx
     path ".command.*"
     path "isec-2-or-more/*.txt"
     path "isec-1-or-more/*.txt", emit: isec
 
     script:
-    vcf_list = vcfs.join(' ')
+    vcf_list = gzvcf.join(' ')
     regions_command = params.use_intersect_regions ? "--regions-file ${intersect_regions}" : ""
     """
     set -euo pipefail
@@ -54,13 +84,13 @@ process intersect_VCFs_BCFtools {
         ${regions_command} \
         ${vcf_list}
     awk '/Using the following file names:/{x=1;next} x' isec-2-or-more/README.txt  \
-        | sed 's/.vcf.gz\$/-intersect.vcf.gz/' \
+        | sed 's/-reorder.vcf.gz\$/-intersect.vcf.gz/' \
         | while read a b c d; do
             mv \$a \$d
             mv \$a.tbi \$d.tbi
             done
     # intersect, keeping all variants, to create presence/absence list of variants in each VCF
-    bcftools isec \
+    bcftools isec --nfiles +1\
         --output-type z \
         --prefix isec-1-or-more \
         ${regions_command} \
@@ -109,7 +139,7 @@ process concat_VCFs_BCFtools {
     path indices
 
     output:
-    path "*concat.vcf", emit: concat_vcf
+    path "*concat.vcf", emit: vcf
     path ".command.*"
 
     script:
@@ -146,7 +176,7 @@ process convert_VCF_vcf2maf {
     val tumor_id
 
     output:
-    path "*.maf", emit: concat_maf
+    path "*.maf", emit: maf
     path ".command.*"
 
     script:
diff --git a/module/intersect.nf b/module/intersect.nf
index 94803ba3..83f6d86b 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -3,8 +3,16 @@ include { compress_file_blarchive} from './common'  addParams(
     blarchive_publishDir : "${params.workflow_output_dir}/output",
     blarchive_enabled : true
     )
-include { intersect_VCFs_BCFtools; plot_VennDiagram_R; concat_VCFs_BCFtools ; convert_VCF_vcf2maf } from './intersect-processes.nf'
-include { compress_index_VCF } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
+include { reorder_samples_BCFtools; intersect_VCFs_BCFtools; plot_VennDiagram_R; concat_VCFs_BCFtools ; convert_VCF_vcf2maf } from './intersect-processes.nf'
+include { compress_index_VCF as compress_index_VCF_reordered } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
+    options: [
+        output_dir: params.workflow_output_dir,
+        log_output_dir: params.workflow_log_output_dir,
+        bgzip_extra_args: params.bgzip_extra_args,
+        tabix_extra_args: params.tabix_extra_args,
+        is_output_file: false
+        ])
+include { compress_index_VCF as compress_index_VCF_concat } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
     options: [
         output_dir: params.workflow_output_dir,
         log_output_dir: params.workflow_log_output_dir,
@@ -16,23 +24,45 @@ def sortVcfs(List paths) {
         def toolA = file(a).getName()
         def toolB = file(b).getName()
         return toolA.compareTo(toolB)
+        }
+    }
+def getToolName(filename) {
+    return file(filename).getName().split('-')[0]
     }
-}
 
 workflow intersect {
     take:
-    tool_vcfs
+    tool_gzvcfs
     tool_indices
     script_dir_ch
     normal_id
     tumor_id
 
     main:
-        vcfs_ch = tool_vcfs
+        tool_gzvcfs_ch = tool_gzvcfs
+            .flatten()
+            .map{ it -> [getToolName(it), it]}
+        tool_indices_ch = tool_indices
+            .flatten()
+        reorder_samples_BCFtools(
+            tool_gzvcfs_ch,
+            tool_indices_ch,
+            normal_id,
+            tumor_id
+            )
+        compress_index_VCF_reordered(reorder_samples_BCFtools.out.gzvcf
+            .map{ it -> ["${getToolName(it)}-SNV", it]}
+            )
+        gzvcfs = compress_index_VCF_reordered.out.index_out
+            .map{ it -> it[1] }
+            .collect()
             .map { sortVcfs(it)  }
+        indices = compress_index_VCF_reordered.out.index_out
+            .map{ it -> it[2] }
+            .collect()
         intersect_VCFs_BCFtools(
-            vcfs_ch,
-            tool_indices,
+            gzvcfs,
+            indices,
             params.intersect_regions,
             params.intersect_regions_index
             )
@@ -40,35 +70,35 @@ workflow intersect {
             script_dir_ch,
             intersect_VCFs_BCFtools.out.isec,
             )
-        intersect_vcfs_ch = intersect_VCFs_BCFtools.out.intersect_vcf
+        intersect_vcfs = intersect_VCFs_BCFtools.out.gzvcf
             .map { sortVcfs(it) }
         concat_VCFs_BCFtools(
-            intersect_vcfs_ch,
-            intersect_VCFs_BCFtools.out.intersect_idx
+            intersect_vcfs,
+            intersect_VCFs_BCFtools.out.idx
             )
         convert_VCF_vcf2maf(
-            concat_VCFs_BCFtools.out.concat_vcf,
+            concat_VCFs_BCFtools.out.vcf,
             params.reference,
             normal_id,
             tumor_id
             )
-        compress_index_VCF(concat_VCFs_BCFtools.out.concat_vcf
+        compress_index_VCF_concat(concat_VCFs_BCFtools.out.vcf
             .map{ it -> ['SNV', it]}
             )
-        compress_file_blarchive(convert_VCF_vcf2maf.out.concat_maf
+        compress_file_blarchive(convert_VCF_vcf2maf.out.maf
             .map{ it -> ['MAF', it]}
             )
-        file_for_sha512 = intersect_VCFs_BCFtools.out.intersect_vcf
+        file_for_sha512 = intersect_VCFs_BCFtools.out.gzvcf
             .flatten()
-            .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-vcf", it]}
-            .mix(intersect_VCFs_BCFtools.out.intersect_idx
+            .map{ it -> ["${getToolName(it)}-vcf", it]}
+            .mix(intersect_VCFs_BCFtools.out.idx
                 .flatten()
-                .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-idx", it]}
+                .map{ it -> ["${getToolName(it)}-idx", it]}
                 )
-            .mix(compress_index_VCF.out.index_out
+            .mix(compress_index_VCF_concat.out.index_out
                 .map{ it -> ["concat-${it[0]}-vcf", it[1]] }
                 )
-            .mix(compress_index_VCF.out.index_out
+            .mix(compress_index_VCF_concat.out.index_out
                 .map{ it -> ["concat-${it[0]}-index", it[2]] }
                 )
             .mix(compress_file_blarchive.out.compressed_file
diff --git a/module/muse-processes.nf b/module/muse-processes.nf
index 2a618362..33a10cb7 100644
--- a/module/muse-processes.nf
+++ b/module/muse-processes.nf
@@ -77,53 +77,3 @@ process run_sump_MuSE {
         -D $dbSNP
     """
     }
-
-process filter_VCF_BCFtools {
-    container params.docker_image_BCFtools
-    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
-        mode: "copy",
-        pattern: "*.vcf.gz",
-        enabled: params.save_intermediate_files
-    publishDir path: "${params.workflow_log_output_dir}",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process.split(':')[-1]}-${var_type}/log${file(it).getName()}" }
-
-    input:
-    tuple val(var_type), path(vcf)
-
-    output:
-    tuple val(var_type), path("*.vcf.gz"), emit: pass_vcf
-    path ".command.*"
-
-    script:
-    """
-    set -euo pipefail
-    bcftools view -f PASS  --output-type z --output ${params.output_filename}_${var_type}-pass.vcf.gz ${vcf}
-    """
-    }
-
-process reorder_samples_BCFtools {
-    container params.docker_image_BCFtools
-    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
-        mode: "copy",
-        pattern: "*.vcf.gz",
-        enabled: params.save_intermediate_files
-    publishDir path: "${params.workflow_log_output_dir}",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process.split(':')[-1]}-${var_type}/log${file(it).getName()}" }
-
-    input:
-    tuple val(var_type), path(vcf)
-
-    output:
-    tuple val(var_type), path("*.vcf.gz"), emit: reorder_vcf
-    path ".command.*"
-
-    script:
-    """
-    set -euo pipefail
-    bcftools view -s NORMAL,TUMOR --output ${params.output_filename}_pass-reorder.vcf.gz ${vcf}
-    """
-    }
diff --git a/module/muse.nf b/module/muse.nf
index 6bf5c9cf..8f45c39c 100644
--- a/module/muse.nf
+++ b/module/muse.nf
@@ -1,5 +1,5 @@
-include { call_sSNV_MuSE; run_sump_MuSE; filter_VCF_BCFtools; reorder_samples_BCFtools } from './muse-processes'
-include { rename_samples_BCFtools; generate_sha512sum } from './common'
+include { call_sSNV_MuSE; run_sump_MuSE } from './muse-processes'
+include { filter_VCF_BCFtools; rename_samples_BCFtools; generate_sha512sum } from './common'
 include { compress_index_VCF } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
     options: [
         output_dir: params.workflow_output_dir,
@@ -31,14 +31,12 @@ workflow muse {
             "${params.dbSNP}.tbi"
         )
         filter_VCF_BCFtools(run_sump_MuSE.out.vcf.map { it -> ['SNV', it] } )
-        // MuSE output VCF has sample order: TUMOR NORMAL, opposite of all other tools. Need to reorder.
-        reorder_samples_BCFtools(filter_VCF_BCFtools.out.pass_vcf)
-        rename_samples_BCFtools(normal_id, tumor_id, reorder_samples_BCFtools.out.reorder_vcf)
-        compress_index_VCF(rename_samples_BCFtools.out.fix_vcf)
+        rename_samples_BCFtools(normal_id, tumor_id, filter_VCF_BCFtools.out.gzvcf)
+        compress_index_VCF(rename_samples_BCFtools.out.gzvcf)
         file_for_sha512 = compress_index_VCF.out.index_out.map{ it -> ["muse-${it[0]}-vcf", it[1]] }
             .mix(compress_index_VCF.out.index_out.map{ it -> ["muse-${it[0]}-index", it[2]] })
         generate_sha512sum(file_for_sha512)
     emit:
-        vcf = compress_index_VCF.out.index_out.map{ it -> ["${it[1]}"] }
+        gzvcf = compress_index_VCF.out.index_out.map{ it -> ["${it[1]}"] }
         idx = compress_index_VCF.out.index_out.map{ it -> ["${it[2]}"] }
     }
diff --git a/module/mutect2-processes.nf b/module/mutect2-processes.nf
index 137d0438..529a8f9f 100644
--- a/module/mutect2-processes.nf
+++ b/module/mutect2-processes.nf
@@ -263,31 +263,6 @@ process run_FilterMutectCalls_GATK {
     """
     }
 
-process filter_VCF_BCFtools {
-    container params.docker_image_BCFtools
-    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
-        mode: "copy",
-        pattern: "*.vcf.gz",
-        enabled: params.save_intermediate_files
-    publishDir path: "${params.workflow_log_output_dir}",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process.split(':')[-1]}-${var_type}/log${file(it).getName()}" }
-
-    input:
-    tuple val(var_type), path(vcf)
-
-    output:
-    tuple val(var_type), path("*.vcf.gz"), emit: pass_vcf
-    path ".command.*"
-
-    script:    
-    """
-    set -euo pipefail
-    bcftools view -f PASS --output-type z --output ${params.output_filename}_${var_type}-pass.vcf.gz ${vcf}
-    """
-    }
-
 process split_VCF_BCFtools {
     container params.docker_image_BCFtools
     publishDir path: "${params.workflow_output_dir}/output",
@@ -303,7 +278,7 @@ process split_VCF_BCFtools {
     each var_type
 
     output:
-    tuple val(var_type), path("*.vcf.gz"), emit: split_vcf
+    tuple val(var_type), path("*.vcf.gz"), emit: gzvcf
     path ".command.*"
 
     script:
diff --git a/module/mutect2.nf b/module/mutect2.nf
index 3d0b92d1..fd245972 100644
--- a/module/mutect2.nf
+++ b/module/mutect2.nf
@@ -1,5 +1,5 @@
-include { run_GetSampleName_Mutect2; run_SplitIntervals_GATK; call_sSNV_Mutect2; run_MergeVcfs_GATK; run_MergeMutectStats_GATK; run_LearnReadOrientationModel_GATK; run_FilterMutectCalls_GATK; filter_VCF_BCFtools; split_VCF_BCFtools } from './mutect2-processes'
-include { generate_sha512sum } from './common'
+include { run_GetSampleName_Mutect2; run_SplitIntervals_GATK; call_sSNV_Mutect2; run_MergeVcfs_GATK; run_MergeMutectStats_GATK; run_LearnReadOrientationModel_GATK; run_FilterMutectCalls_GATK; split_VCF_BCFtools } from './mutect2-processes'
+include { filter_VCF_BCFtools; generate_sha512sum } from './common'
 include { compress_index_VCF } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
     options: [
         output_dir: params.workflow_output_dir,
@@ -92,13 +92,13 @@ workflow mutect2 {
             contamination_table.collect()
         )
         filter_VCF_BCFtools(run_FilterMutectCalls_GATK.out.filtered.map{ it -> ['all', it] })
-        split_VCF_BCFtools(filter_VCF_BCFtools.out.pass_vcf.map{ it -> it[1] }, ['snps', 'mnps', 'indels'])
-        compress_index_VCF(split_VCF_BCFtools.out.split_vcf)
+        split_VCF_BCFtools(filter_VCF_BCFtools.out.gzvcf.map{ it -> it[1] }, ['snps', 'mnps', 'indels'])
+        compress_index_VCF(split_VCF_BCFtools.out.gzvcf)
         file_for_sha512 = compress_index_VCF.out.index_out.map{ it -> ["mutect2-${it[0]}-vcf", it[1]] }
             .mix( compress_index_VCF.out.index_out.map{ it -> ["mutect2-${it[0]}-index", it[2]] } )
         generate_sha512sum(file_for_sha512)
     emit:
-        vcf = compress_index_VCF.out.index_out
+        gzvcf = compress_index_VCF.out.index_out
             .filter { it[0] == 'snps' }
             .map{ it -> ["${it[1]}"] }
         idx = compress_index_VCF.out.index_out
diff --git a/module/somaticsniper-processes.nf b/module/somaticsniper-processes.nf
index f7b6f5b1..da2cfc21 100644
--- a/module/somaticsniper-processes.nf
+++ b/module/somaticsniper-processes.nf
@@ -280,8 +280,8 @@ process call_HighConfidenceSNV_SomaticSniper {
     path fp_pass
 
     output:
-    path "*_hc.vcf", emit: hc
-    path "*_lc.vcf", emit: lc
+    path "*_hc.vcf", emit: hc_vcf
+    path "*_lc.vcf"
     path ".command.*"
 
     """
diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf
index e6a34f5f..a4644c6f 100644
--- a/module/somaticsniper.nf
+++ b/module/somaticsniper.nf
@@ -62,11 +62,11 @@ workflow somaticsniper {
                 .map{ it -> ['readcount', it[0]] }
             )
         // rename_samples_BCFtools needs bgzipped input
-        compress_index_VCF_hc(call_HighConfidenceSNV_SomaticSniper.out.hc
+        compress_index_VCF_hc(call_HighConfidenceSNV_SomaticSniper.out.hc_vcf
             .map{ it -> ['SNV', it] })
         rename_samples_BCFtools(normal_id, tumor_id, compress_index_VCF_hc.out.index_out
             .map{ it -> [it[0], it[1]] })
-        compress_index_VCF_fix(rename_samples_BCFtools.out.fix_vcf)
+        compress_index_VCF_fix(rename_samples_BCFtools.out.gzvcf)
         file_for_sha512 = compress_index_VCF_fix.out.index_out
             .map{ it -> ["${it[0]}-vcf", it[1]] }
             .mix(compress_index_VCF_fix.out.index_out
@@ -74,6 +74,6 @@ workflow somaticsniper {
                 )
         generate_sha512sum(file_for_sha512)
     emit:
-        vcf = compress_index_VCF_fix.out.index_out.map{ it -> ["${it[1]}"] }
+        gzvcf = compress_index_VCF_fix.out.index_out.map{ it -> ["${it[1]}"] }
         idx = compress_index_VCF_fix.out.index_out.map{ it -> ["${it[2]}"] }
     }
diff --git a/module/strelka2-processes.nf b/module/strelka2-processes.nf
index d3bb020d..427febfd 100644
--- a/module/strelka2-processes.nf
+++ b/module/strelka2-processes.nf
@@ -76,8 +76,8 @@ process call_sSNV_Strelka2 {
     path intersect_regions_index
 
     output:
-    tuple val("SNV"), path("StrelkaSomaticWorkflow/results/variants/somatic.snvs.vcf.gz"), emit: snvs_vcf
-    tuple val("Indel"), path("StrelkaSomaticWorkflow/results/variants/somatic.indels.vcf.gz"), emit: indels_vcf
+    tuple val("SNV"), path("StrelkaSomaticWorkflow/results/variants/somatic.snvs.vcf.gz"), emit: snvs_gzvcf
+    tuple val("Indel"), path("StrelkaSomaticWorkflow/results/variants/somatic.indels.vcf.gz"), emit: indels_gzvcf
     path "StrelkaSomaticWorkflow"
     path ".command.*"
 
@@ -98,28 +98,3 @@ process call_sSNV_Strelka2 {
     StrelkaSomaticWorkflow/runWorkflow.py -m local -j ${task.cpus}
     """
     }
-
-process filter_VCF_BCFtools {
-    container params.docker_image_BCFtools
-    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
-        mode: "copy",
-        pattern: "*.vcf.gz",
-        enabled: params.save_intermediate_files
-    publishDir path: "${params.workflow_log_output_dir}",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process.split(':')[-1]}-${var_type}/log${file(it).getName()}" }
-
-    input:
-    tuple val(var_type), path(vcf)
-
-    output:
-    tuple val(var_type), path("*.vcf.gz"), emit: pass_vcf
-    path ".command.*"
-
-    script:
-    """
-    set -euo pipefail
-    bcftools view -f PASS  --output-type z --output ${params.output_filename}_${var_type}-pass.vcf.gz ${vcf}
-    """
-    }
diff --git a/module/strelka2.nf b/module/strelka2.nf
index 429dc997..01424aa4 100644
--- a/module/strelka2.nf
+++ b/module/strelka2.nf
@@ -1,5 +1,5 @@
-include { call_sSNV_Strelka2; call_sIndel_Manta; filter_VCF_BCFtools } from './strelka2-processes'
-include { rename_samples_BCFtools; generate_sha512sum } from './common'
+include { call_sSNV_Strelka2; call_sIndel_Manta } from './strelka2-processes'
+include { filter_VCF_BCFtools; rename_samples_BCFtools; generate_sha512sum } from './common'
 
 include { compress_index_VCF } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
     options: [
@@ -40,21 +40,20 @@ workflow strelka2 {
             params.intersect_regions,
             params.intersect_regions_index
         )
-        filter_VCF_BCFtools(call_sSNV_Strelka2.out.snvs_vcf
-            .mix(call_sSNV_Strelka2.out.indels_vcf))
-        normal_id.combine(filter_VCF_BCFtools.out.pass_vcf).map{ it[0] }.set{ normal_id_fix }
-        tumor_id.combine(filter_VCF_BCFtools.out.pass_vcf).map{ it[0] }.set{ tumor_id_fix }
-        rename_samples_BCFtools(normal_id_fix, tumor_id_fix, filter_VCF_BCFtools.out.pass_vcf)
-        compress_index_VCF(rename_samples_BCFtools.out.fix_vcf)
+        filter_VCF_BCFtools(call_sSNV_Strelka2.out.snvs_gzvcf
+            .mix(call_sSNV_Strelka2.out.indels_gzvcf))
+        normal_id.combine(filter_VCF_BCFtools.out.gzvcf).map{ it[0] }.set{ normal_id_fix }
+        tumor_id.combine(filter_VCF_BCFtools.out.gzvcf).map{ it[0] }.set{ tumor_id_fix }
+        rename_samples_BCFtools(normal_id_fix, tumor_id_fix, filter_VCF_BCFtools.out.gzvcf)
+        compress_index_VCF(rename_samples_BCFtools.out.gzvcf)
         file_for_sha512 = compress_index_VCF.out.index_out.map{ it -> ["strelka2-${it[0]}-vcf", it[1]] }
             .mix( compress_index_VCF.out.index_out.map{ it -> ["strelka2-${it[0]}-index", it[2]] } )
         generate_sha512sum(file_for_sha512)
     emit:
-        vcf = compress_index_VCF.out.index_out
+        gzvcf = compress_index_VCF.out.index_out
             .filter { it[0] == 'SNV' }
             .map{ it -> ["${it[1]}"] }
         idx = compress_index_VCF.out.index_out
             .filter { it[0] == 'SNV' }
             .map{ it -> ["${it[2]}"] }
-
     }
diff --git a/nftest.yml b/nftest.yml
index 04c206e8..3e031f17 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -130,6 +130,62 @@ cases:
         expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/TWGSAMIN000001/Mutect2-4.4.0.0/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
         script: test/assert_vcf.sh
 
+  - name: a_mini-two-tools
+    message: test development branch using somaticsniper and strelka2 with standard paired tumor and normal a-mini-n2 input
+    nf_script: ./main.nf
+    nf_config: ./test/config/a_mini-two-tools.config
+    params_file: ./test/yaml/a_mini_n2-std-input.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/SomaticSniper-1.0.5.0/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz
+        script: test/assert_vcf.sh
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Indel.vcf.gz
+        script: test/assert_vcf.sh
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Strelka2-2.9.10/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV.vcf.gz
+        script: test/assert_vcf.sh
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.vcf.gz
+        script: test/assert_vcf.sh
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-concat.maf.bz2
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_Venn-diagram.tiff
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-1-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_README.txt
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/isec-2-or-more/BCFtools-1.17_TWGSAMIN_TWGSAMIN000001-T001-S01-F_sites.txt
+        method: md5
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/SomaticSniper-1.0.5.0_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz
+        script: test/assert_vcf.sh
+
+      - actual: call-sSNV-7.0.0-rc.1/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/TWGSAMIN000001-T001-S01-F/Intersect-BCFtools-1.17/Strelka2-2.9.10_TWGSAMIN_TWGSAMIN000001-T001-S01-F_SNV-intersect.vcf.gz
+        script: test/assert_vcf.sh
+
   - name: a_mini-somaticsniper
     message: test development branch using somaticsniper and standard paired tumor and normal a-mini-n2 input
     nf_script: ./main.nf
diff --git a/test/config/a_mini-two-tools.config b/test/config/a_mini-two-tools.config
new file mode 100644
index 00000000..d1ca0db5
--- /dev/null
+++ b/test/config/a_mini-two-tools.config
@@ -0,0 +1,41 @@
+/**
+*       EXECUTION SETTINGS AND GLOBAL DEFAULTS
+*       External config files import. DO NOT MODIFY THIS LINE!
+*/
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/nextflow.config"
+includeConfig "${projectDir}/config/methods.config"
+
+/**
+*       Inputs/parameters of the pipeline
+*/
+
+params {
+    algorithm = ['somaticsniper', 'strelka2']
+    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    dataset_id = 'TWGSAMIN'
+     // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE
+    exome = false
+    save_intermediate_files = false
+
+    // module options
+    bgzip_extra_args = ''
+    tabix_extra_args = ''
+
+    // mutect2 options
+    split_intervals_extra_args = ''
+    mutect2_extra_args = ''
+    filter_mutect_calls_extra_args = ''
+    gatk_command_mem_diff = 500.MB
+    scatter_count = 12
+    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+
+    // MuSE options
+    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+
+    // Intersect options
+    ncbi_build = 'GRCh38'
+    vcf2maf_extra_args = ''
+}
+methods.setup()