Merge pull request #877 from milaboratory/use_local_temp

Use local temp
milaboratory · Nov 9, 2022 · b1f6ec6 · b1f6ec6
2 parents 0821262 + c6a4269
commit b1f6ec6
Show file tree

Hide file tree

Showing 10 changed files with 280 additions and 162 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -101,7 +101,7 @@ repositories {
 val milibVersion = "2.1.0"
 val repseqioVersion = "1.5.0"
 val miplotsVersion = "1.1.0"
-val mitoolVersion = "1.2.0-11-main"
+val mitoolVersion = "1.2.0-15-main"
 val jacksonBomVersion = "2.14.0"
 val redberryPipeVersion = "1.3.0"
 

diff --git a/itests/case-usage_of_template.sh b/itests/case-usage_of_template.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+mixcr analyze generic-tcr-amplicon \
+  --species hs \
+  --rna \
+  --floating-left-alignment-boundary \
+  --floating-right-alignment-boundary J \
+  --add-step assembleContigs \
+  test_{{R}}.fastq result_1
+
+[[ -f result_1.clna ]] || exit 1
+
+mixcr align -p generic-tcr-amplicon \
+  --species hs \
+  --rna \
+  --floating-left-alignment-boundary \
+  --floating-right-alignment-boundary J \
+  test_{{R}}.fastq result_2.vdjca
+
+[[ -f result_2.vdjca ]] || exit 1
diff --git a/src/main/kotlin/com/milaboratory/mixcr/MiXCRCommandDescriptor.kt b/src/main/kotlin/com/milaboratory/mixcr/MiXCRCommandDescriptor.kt
@@ -70,6 +70,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
     abstract val command: String
     abstract val order: Int
     abstract val hasThreadsOption: Boolean
+    abstract val hasUseLocalTempOption: Boolean
     open val allowMultipleRounds: Boolean get() = false
 
     abstract fun outputName(prefix: String, params: P, round: Int): String
@@ -112,6 +113,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val order get() = 0
 
         override val hasThreadsOption = true
+        override val hasUseLocalTempOption = false
 
         override fun outputName(prefix: String, params: CommandAlign.Params, round: Int) =
             "${prefix.ifBlank { "alignments" }}.vdjca"
@@ -130,6 +132,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = RefineTagsAndSortReport::class
 
         override val hasThreadsOption = false
+        override val hasUseLocalTempOption = true
 
         @get:JsonValue
         override val command get() = CommandRefineTagsAndSort.COMMAND_NAME
@@ -152,6 +155,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = NoReport::class
 
         override val hasThreadsOption = false
+        override val hasUseLocalTempOption = false
 
         @get:JsonValue
         override val command get() = CommandExportAlignments.COMMAND_NAME
@@ -171,6 +175,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = PartialAlignmentsAssemblerReport::class
 
         override val hasThreadsOption = false
+        override val hasUseLocalTempOption = false
 
         @get:JsonValue
         override val command get() = CommandAssemblePartial.COMMAND_NAME
@@ -194,6 +199,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = VDJCObjectExtenderReport::class
 
         override val hasThreadsOption = true
+        override val hasUseLocalTempOption = false
 
         @get:JsonValue
         override val command get() = CommandExtend.COMMAND_NAME
@@ -216,6 +222,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = CloneAssemblerReport::class
 
         override val hasThreadsOption = false
+        override val hasUseLocalTempOption = true
 
         @get:JsonValue
         override val command get() = CommandAssemble.COMMAND_NAME
@@ -238,6 +245,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = FullSeqAssemblerReport::class
 
         override val hasThreadsOption = true
+        override val hasUseLocalTempOption = false
 
         @get:JsonValue
         override val command get() = CommandAssembleContigs.COMMAND_NAME
@@ -260,6 +268,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = NoReport::class
 
         override val hasThreadsOption = false
+        override val hasUseLocalTempOption = false
 
         @get:JsonValue
         override val command get() = CommandExportClones.COMMAND_NAME
@@ -279,6 +288,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = FindAllelesReport::class
 
         override val hasThreadsOption = true
+        override val hasUseLocalTempOption = true
 
         @get:JsonValue
         override val command get() = CommandFindAlleles.COMMAND_NAME
@@ -297,6 +307,7 @@ sealed class MiXCRCommandDescriptor<P : MiXCRParams, R : MiXCRCommandReport> : C
         override val reportClass get() = BuildSHMTreeReport::class
 
         override val hasThreadsOption = true
+        override val hasUseLocalTempOption = true
 
         @get:JsonValue
         override val command get() = CommandFindShmTrees.COMMAND_NAME