Merge pull request #325 from uclahs-cds/sfitz-fix-single-tool-runs

Sfitz fix single tool runs
uclahs-cds · Nov 22, 2024 · 89998db · 89998db
2 parents 248c58a + fda0412
commit 89998db
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Showing 4 changed files with 36 additions and 33 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 ### Changed
+- Update NFTest paths
+- Fix single tool run logic
 - Update PipeVal 4.0.0-rc.2 -> 5.1.0
 - Update GATK 4.5.0.0 -> 4.6.1.0
 - Update bam_readcount 0.8.0 -> 1.0.1

diff --git a/main.nf b/main.nf
@@ -232,30 +232,31 @@ workflow {
             mutect2.out.gzvcf.set { mutect2_gzvcf_ch }
             mutect2.out.idx.set { mutect2_idx_ch }
             }
-        // Intersect all vcf files
-        if (params.algorithm.size() > 1) {
-            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()
-            }
+
+        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()
+
     } else if (params.input_type == 'vcf') {
         process_vcfs(samplesToProcess_ch)
         process_vcfs.out.gzvcf.set { tool_gzvcfs }
         process_vcfs.out.idx.set { tool_indices }
         }
 
-    intersect(
-        tool_gzvcfs,
-        tool_indices,
-        script_dir_ch,
-        )
+    if (params.algorithm.size() > 1 || params.input_type == 'vcf') {
+        intersect(
+            tool_gzvcfs,
+            tool_indices,
+            script_dir_ch,
+            )
+        }
 
     all_files = tool_gzvcfs.mix(tool_indices)
         .flatten()

diff --git a/nftest.yml b/nftest.yml
@@ -91,15 +91,15 @@ cases:
     verbose: true
     asserts:
       - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_Indel.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_MNV.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Mutect2-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-tumor-only/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV.vcf.gz
         script: test/assert_vcf.sh
 
   - name: a_mini-mutect2-multiple-samples
@@ -111,15 +111,15 @@ cases:
     verbose: true
     asserts:
       - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.4.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_Indel.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.4.0.0_TWGSAMIN_TWGSAMIN000001_MNV.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/TWGSAMIN000001/Mutect2-*/output/Mutect2-*_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-mutect2-multiple-samples/Mutect2-4.6.1.0_TWGSAMIN_TWGSAMIN000001_SNV.vcf.gz
         script: test/assert_vcf.sh
 
   - name: a_mini-two-tools
@@ -143,31 +143,31 @@ cases:
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_SNV-concat.maf.bz2
         method: md5
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/BCFtools-*_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_Venn-diagram.tiff
         method: md5
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-1-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/isec-1-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
         method: md5
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/isec-2-or-more/BCFtools-*_TWGSAMIN_S2-v1.1.5_sites.txt
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/isec-2-or-more/BCFtools-1.17_TWGSAMIN_S2-v1.1.5_sites.txt
         method: md5
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Strelka2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/a_mini-two-tools/Intersect-BCFtools/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
         script: test/assert_vcf.sh
 
   - name: a_mini-somaticsniper
@@ -263,7 +263,7 @@ cases:
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/Mutect2-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.4.0.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-output/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz
         script: test/assert_vcf.sh
 
       - actual: call-sSNV-*/S2-v1.1.5/Intersect-BCFtools-*/output/SomaticSniper-*_TWGSAMIN_S2-v1.1.5_SNV-intersect.vcf.gz

diff --git a/test/yaml/a_mini-vcf.yaml b/test/yaml/a_mini-vcf.yaml
@@ -5,6 +5,6 @@ input_tumor_id: 'S2_v1.1.5' # tumor ID in the VCF files must match this or 'TUMO
 input_normal_id: 'HG002.N' # normal ID in the VCF files must match this or 'NORMAL'
 input:
   muse: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/MuSE-2.0.4_TWGSAMIN_S2-v1.1.5_SNV-pass.vcf.gz
-  mutect2: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/Mutect2-4.5.0.0_TWGSAMIN_S2-v1.1.5_all-pass.vcf.gz
+  mutect2: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/Mutect2-4.6.1.0_TWGSAMIN_S2-v1.1.5_all-pass.vcf.gz
   somaticsniper: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/SomaticSniper-1.0.5.0_TWGSAMIN_S2-v1.1.5_hc.vcf.gz
   strelka2: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/Strelka2-2.9.10_TWGSAMIN_S2-v1.1.5_SNV-pass.vcf.gz