nf-core · ramprasadn · Jan 31, 2024 · Jan 30, 2024 · Jan 31, 2024 · Jan 31, 2024
diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config
@@ -28,6 +28,23 @@ process {
         ext.prefix = { "${meta.id}_exphunter" }
     }
 
+    withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT' {
+        ext.prefix = { "${meta.id}_exphunter_sorted" }
+        publishDir = [
+            path: { "${params.outdir}/repeat_expansions" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_INDEX' {
+        publishDir = [
+            path: { "${params.outdir}/repeat_expansions" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' {
         ext.args = "--temp-prefix ."
         ext.prefix = { "${meta.id}_reheader" }
@@ -66,7 +83,7 @@ process {
     }
 
     withName: '.*CALL_REPEAT_EXPANSIONS:COMPRESS_STRANGER' {
-        ext.prefix = { "${meta.id}_repeat_expansion" }
+        ext.prefix = { "${meta.id}_repeat_expansion_stranger" }
         ext.args   = '--output-type z'
         publishDir = [
             path: { "${params.outdir}/repeat_expansions" },

diff --git a/docs/output.md b/docs/output.md
@@ -301,6 +301,10 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.
 - `repeat_expansions/`
   - `<sample_id>_repeat_expansion.vcf.gz`: file containing variant calls.
   - `<sample_id>_repeat_expansion.vcf.gz.tbi`: index of the file containing variant calls.
+  - `<sample_id>_exphunter_sorted.bam`: A BAMlet containing alignments of reads that overlap or located in close proximity to each variant identified by ExpansionHunter
+  - `<sample_id>_exphunter_sorted.bam.bai`: Index of the BAMlet file
+  - `<case_id>_repeat_expansion_stranger.vcf.gz`: Output from ExpansionHunter annotated with the pathologic implications of the repeat sizes by Stranger.
+  - `<case_id>_repeat_expansion_stranger.vcf.gz`: Index of the Stranger VCF file.
 
 </details>
 

diff --git a/modules.json b/modules.json
@@ -123,7 +123,7 @@
                     },
                     "expansionhunter": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "3c4b0007393248aa7419a9ec3d14f391cd702f48",
                         "installed_by": ["modules"]
                     },
                     "fastp": {

diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf
diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml
diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test b/modules/nf-core/expansionhunter/tests/main.nf.test
diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test.snap b/modules/nf-core/expansionhunter/tests/main.nf.test.snap
diff --git a/modules/nf-core/expansionhunter/tests/tags.yml b/modules/nf-core/expansionhunter/tests/tags.yml
diff --git a/subworkflows/local/call_repeat_expansions.nf b/subworkflows/local/call_repeat_expansions.nf
@@ -8,6 +8,8 @@ include { BCFTOOLS_VIEW as COMPRESS_STRANGER           } from '../../modules/nf-
 include { EXPANSIONHUNTER                              } from '../../modules/nf-core/expansionhunter/main'
 include { PICARD_RENAMESAMPLEINVCF as RENAMESAMPLE_EXP } from '../../modules/nf-core/picard/renamesampleinvcf/main'
 include { STRANGER                                     } from '../../modules/nf-core/stranger/main'
+include { SAMTOOLS_SORT                                } from '../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX                               } from '../../modules/nf-core/samtools/index/main'
 include { SVDB_MERGE as SVDB_MERGE_REPEATS             } from '../../modules/nf-core/svdb/merge/main'
 include { TABIX_BGZIPTABIX as BGZIPTABIX_EXP           } from '../../modules/nf-core/tabix/bgziptabix/main'
 include { TABIX_TABIX as INDEX_STRANGER                } from '../../modules/nf-core/tabix/tabix/main'
@@ -31,6 +33,10 @@ workflow CALL_REPEAT_EXPANSIONS {
             ch_variant_catalog
         )
 
+        // Sort and index realigned bam
+        SAMTOOLS_SORT(EXPANSIONHUNTER.out.bam)
+        SAMTOOLS_INDEX(SAMTOOLS_SORT.out.bam)
+
         // Fix header and rename sample
         BCFTOOLS_REHEADER_EXP (
             EXPANSIONHUNTER.out.vcf.map{ meta, vcf -> [ meta, vcf, [], [] ]},
@@ -77,6 +83,8 @@ workflow CALL_REPEAT_EXPANSIONS {
         ch_versions = ch_versions.mix(STRANGER.out.versions.first())
         ch_versions = ch_versions.mix(COMPRESS_STRANGER.out.versions.first())
         ch_versions = ch_versions.mix(INDEX_STRANGER.out.versions.first())
+        ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
 emit:
         vcf      = ch_vcf_idx  // channel: [ val(meta), path(vcf), path(tbi) ]