Add bwameme

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new aligner, bwameme [#553](https://github.com/nf-core/raredisease/pull/553)
 - A new parameter `run_mt_for_wes` to turn on mitochondrial analysis for targeted analysis [#552](https://github.com/nf-core/raredisease/pull/552)
 - A new parameter `bwa_as_fallback` to switch aligner to bwa in case bwamem2 fails [#551](https://github.com/nf-core/raredisease/pull/551)
 
@@ -25,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Old parameter | New parameter   |
 | ------------- | --------------- |
+|               | bwameme         |
 |               | bwa_as_fallback |
 |               | run_mt_for_wes  |
 

conf/modules/align_MT.config

@@ -19,16 +19,25 @@ process {
 
     withName: '.*ALIGN_MT:BWAMEM2_MEM_MT' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
+        ext.prefix = { "${meta.id}_sorted" }
+    }
+
+    withName: '.*ALIGN_MT:BWAMEME_MEM_MT' {
+        ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
     withName: '.*ALIGN_MT:BWA_MEM_MT' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
     withName: '.*ALIGN_MT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
@@ -67,16 +76,25 @@ process {
 
     withName: '.*ALIGN_MT_SHIFT:BWAMEM2_MEM_MT' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
+        ext.prefix = { "${meta.id}_sorted_shifted" }
+    }
+
+    withName: '.*ALIGN_MT_SHIFT:BWAMEME_MEM_MT' {
+        ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
     withName: '.*ALIGN_MT_SHIFT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 
     withName: '.*ALIGN_MT_SHIFT:BWA_MEM_MT' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted_shifted" }
     }
 

conf/modules/align_bwa_bwamem2.config → conf/modules/align_bwa_bwamem2_bwameme.config

@@ -17,33 +17,40 @@
 
 process {
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM2_MEM' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM_FALLBACK' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM_FALLBACK' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM' {
+        ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
+        ext.prefix = { "${meta.id}_sorted" }
+        ext.when = { params.aligner.equals("bwameme") }
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWA_MEM' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_STATS' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS' {
         ext.args = '-s --remove-overlaps'
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_MERGE' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_MERGE' {
         ext.prefix = { "${meta.id}_sorted_merged" }
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:MARKDUPLICATES' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES' {
         ext.args = "--TMP_DIR ."
         ext.prefix = { "${meta.id}_sorted_md" }
         publishDir = [
@@ -54,7 +61,7 @@ process {
         ]
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_INDEX_MARKDUP' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' {
         publishDir = [
             enabled: !params.save_mapped_as_cram,
             path: { "${params.outdir}/alignment" },

conf/modules/prepare_references.config

@@ -29,10 +29,20 @@ process {
         ext.when = {!params.bwamem2 && params.aligner == "bwamem2"}
     }
 
+    withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' {
+        ext.args = '-a meme'
+        ext.when = {!params.bwameme && params.aligner == "bwameme"}
+    }
+
     withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' {
         ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.aligner == "bwamem2"}
     }
 
+    withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_MT_SHIFT' {
+        ext.args = '-a meme'
+        ext.when = { !(params.analysis_type == "wes") && params.aligner == "bwameme"}
+    }
+
     withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' {
         ext.when = {!params.bwa && params.aligner == "sentieon"}
     }