Merge branch 'dev' into inputschemafixes

nf-core · May 20, 2024 · 8b380e3 · 8b380e3
2 parents 40c1e5e + 5e7b87e
commit 8b380e3
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Showing 5 changed files with 34 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new parameter `bwa_as_fallback` to switch aligner to bwa in case bwamem2 fails [#551](https://github.com/nf-core/raredisease/pull/551)
+
 ### `Changed`
 
 - Changed valid values for sex according to the PED file format [#550](https://github.com/nf-core/raredisease/pull/550)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
@@ -21,14 +21,18 @@ process {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
-        ext.when = { params.aligner.equals("bwamem2") }
+    }
+
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2: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' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
-        ext.when = { params.aligner.equals("bwa") }
     }
 
     withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:SAMTOOLS_STATS' {

diff --git a/nextflow.config b/nextflow.config
@@ -22,6 +22,7 @@ params {
 
     // Main options
     analysis_type              = 'wgs'
+    bwa_as_fallback            = false
     bait_padding               = 100
     run_rtgvcfeval             = false
     save_mapped_as_cram        = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -465,6 +465,12 @@
                     "fa_icon": "fas fa-align-center",
                     "enum": ["wgs", "wes", "mito"]
                 },
+                "bwa_as_fallback": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
+                    "help_text": "errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "platform": {
                     "type": "string",
                     "default": "illumina",

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -3,6 +3,7 @@
 //
 
 include { BWA_MEM                                  } from '../../../modules/nf-core/bwa/mem/main'
+include { BWA_MEM as BWAMEM_FALLBACK               } from '../../../modules/nf-core/bwa/mem/main'
 include { BWAMEM2_MEM                              } from '../../../modules/nf-core/bwamem2/mem/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGN   } from '../../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MARKDUP } from '../../../modules/nf-core/samtools/index/main'
@@ -30,8 +31,25 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
         } else {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
-            ch_align = BWAMEM2_MEM.out.bam
+            ch_align    = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+
+            if (params.bwa_as_fallback) {
+                ch_reads_input
+                    .join(BWAMEM2_MEM.out.bam, remainder: true)
+                    .branch { it ->
+                        ERROR: it[2].equals(null)
+                            return [it[0], it[1]] // return reads
+                        SUCCESS: !it[2].equals(null)
+                            return [it[0], it[2]]  // return bam
+                    }
+                    .set { ch_fallback }
+
+                BWAMEM_FALLBACK ( ch_fallback.ERROR, ch_bwa_index, true )
+                ch_align = ch_fallback.SUCCESS.mix(BWAMEM_FALLBACK.out.bam)
+                ch_versions = ch_versions.mix(BWAMEM_FALLBACK.out.versions.first())
+            }
+
         }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )