Merge pull request #102 from uclahs-cds/maotian-fix-interval-bug

Fix the interval list input bug
uclahs-cds · Jun 23, 2022 · fbfa5ad · fbfa5ad
2 parents f98b3eb + b8e5179
commit fbfa5ad
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 - Fix the bug with M64 detection.
+- Fix the bug with interval list input.
 
 ## [4.0.0] - 2022-06-13
 ### Changed

diff --git a/module/mutect2.nf b/module/mutect2.nf
@@ -81,24 +81,22 @@ workflow mutect2 {
         )
 
         if (params.intervals) {
-            run_MergeVcfs_GATK(call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered.collect())
-            run_MergeMutectStats_GATK(
-                call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered_stats.collect())
+            ich_MergeVcfs = call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered.collect()
+            ich_MergeMutectStats = call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered_stats.collect()
+            ich_LearnReadOrientationModel = call_sSNVInAssembledChromosomes_Mutect2.out.f1r2.collect()
         } else {
-            run_MergeVcfs_GATK(call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered.mix(
-                call_sSNVInNonAssembledChromosomes_Mutect2.out.unfiltered
-                ).collect())
-            run_MergeMutectStats_GATK(
-                call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered_stats.mix(
-                    call_sSNVInNonAssembledChromosomes_Mutect2.out.unfiltered_stats
-                    ).collect()
-            )
+            ich_MergeVcfs = call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered.mix(
+                call_sSNVInNonAssembledChromosomes_Mutect2.out.unfiltered).collect()
+            ich_MergeMutectStats = call_sSNVInAssembledChromosomes_Mutect2.out.unfiltered_stats.mix(
+                call_sSNVInNonAssembledChromosomes_Mutect2.out.unfiltered_stats).collect()
+            ich_LearnReadOrientationModel = call_sSNVInAssembledChromosomes_Mutect2.out.f1r2.mix(
+                call_sSNVInNonAssembledChromosomes_Mutect2.out.f1r2).collect()
         }
-        run_LearnReadOrientationModel_GATK(
-            call_sSNVInAssembledChromosomes_Mutect2.out.f1r2.mix(
-                call_sSNVInNonAssembledChromosomes_Mutect2.out.f1r2
-                ).collect()
-        )
+
+        run_MergeVcfs_GATK(ich_MergeVcfs)
+        run_MergeMutectStats_GATK(ich_MergeMutectStats)
+        run_LearnReadOrientationModel_GATK(ich_LearnReadOrientationModel)
+
         run_FilterMutectCalls_GATK(
             params.reference,
             params.reference_index,