Merge pull request #365 from genomic-medicine-sweden/add_ek

Add ek
nf-core · Jun 26, 2023 · dc29093 · dc29093
2 parents f5ccf9c + 0b34b25
commit dc29093
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Showing 7 changed files with 157 additions and 22 deletions.
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -32,6 +32,10 @@
 
   > Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235
 
+- [eKLIPse](https://www.nature.com/articles/s41436-018-0350-8)
+
+  > Goudenège D, Bris C, Hoffmann V, et al. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 21, 1407–1416 (2019). doi:10.1038/s41436-018-0350-8
+
 - [Ensembl VEP](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4)
 
   > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4

diff --git a/README.md b/README.md
@@ -70,8 +70,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
 **7. Mitochondrial analysis:**
 
 - [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)
+- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)
 - Annotation:
   - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)
+  - [Hmtnote](https://github.com/robertopreste/HmtNote)
   - [vcfanno](https://github.com/brentp/vcfanno)
   - [CADD](https://cadd.gs.washington.edu/)
   - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)

diff --git a/modules.json b/modules.json
@@ -80,6 +80,11 @@
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
                         "installed_by": ["modules"]
                     },
+                    "eklipse": {
+                        "branch": "master",
+                        "git_sha": "99d437bd91f8509d0460b7abbde47fa430055ecb",
+                        "installed_by": ["modules"]
+                    },
                     "expansionhunter": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",

diff --git a/modules/nf-core/eklipse/main.nf b/modules/nf-core/eklipse/main.nf
diff --git a/modules/nf-core/eklipse/meta.yml b/modules/nf-core/eklipse/meta.yml
diff --git a/subworkflows/local/analyse_MT.nf b/subworkflows/local/analyse_MT.nf
@@ -98,18 +98,21 @@ workflow ANALYSE_MT {
         ch_versions = ch_versions.mix(MERGE_ANNOTATE_MT.out.versions)
 
     emit:
-        vcf           = MERGE_ANNOTATE_MT.out.vcf              // channel: [ val(meta), path(vcf) ]
-        tbi           = MERGE_ANNOTATE_MT.out.tbi              // channel: [ val(meta), path(tbi) ]
-        stats         = ALIGN_AND_CALL_MT.out.stats            // channel: [ val(meta), path(stats) ]
-        filt_stats    = ALIGN_AND_CALL_MT.out.filt_stats       // channel: [ val(meta), path(tsv) ]
-        mt_del_result = ALIGN_AND_CALL_MT.out.mt_del_result    // channel: [ val(meta), path(txt) ]
-        stats_sh      = ALIGN_AND_CALL_MT_SHIFT.out.stats      // channel: [ val(meta), path(stats) ]
-        filt_stats_sh = ALIGN_AND_CALL_MT_SHIFT.out.filt_stats // channel: [ val(meta), path(tsv) ]
-        haplog        = MERGE_ANNOTATE_MT.out.haplog           // channel: [ val(meta), path(txt) ]
-        report        = MERGE_ANNOTATE_MT.out.report           // channel: [ path(html) ]
-        txt           = ALIGN_AND_CALL_MT.out.txt              // channel: [ val(meta), path(txt) ]
-        html          = ALIGN_AND_CALL_MT.out.html             // channel: [ val(meta), path(html) ]
-        txt_sh        = ALIGN_AND_CALL_MT_SHIFT.out.txt        // channel: [ val(meta), path(txt) ]
-        html_sh       = ALIGN_AND_CALL_MT_SHIFT.out.html       // channel: [ val(meta), path(html) ]
-        versions      = ch_versions                            // channel: [ path(versions.yml) ]
+        vcf            = MERGE_ANNOTATE_MT.out.vcf              // channel: [ val(meta), path(vcf) ]
+        tbi            = MERGE_ANNOTATE_MT.out.tbi              // channel: [ val(meta), path(tbi) ]
+        stats          = ALIGN_AND_CALL_MT.out.stats            // channel: [ val(meta), path(stats) ]
+        filt_stats     = ALIGN_AND_CALL_MT.out.filt_stats       // channel: [ val(meta), path(tsv) ]
+        mt_del_result  = ALIGN_AND_CALL_MT.out.mt_del_result    // channel: [ val(meta), path(txt) ]
+        stats_sh       = ALIGN_AND_CALL_MT_SHIFT.out.stats      // channel: [ val(meta), path(stats) ]
+        filt_stats_sh  = ALIGN_AND_CALL_MT_SHIFT.out.filt_stats // channel: [ val(meta), path(tsv) ]
+        eklipse_del    = ALIGN_AND_CALL_MT.out.eklipse_del      // channel: [ val(meta), path(csv) ]
+        eklipse_genes  = ALIGN_AND_CALL_MT.out.eklipse_genes    // channel: [ val(meta), path(csv) ]
+        eklipse_circos = ALIGN_AND_CALL_MT.out.eklipse_circos   // channel: [ val(meta), path(png) ]
+        haplog         = MERGE_ANNOTATE_MT.out.haplog           // channel: [ val(meta), path(txt) ]
+        report         = MERGE_ANNOTATE_MT.out.report           // channel: [ path(html) ]
+        txt            = ALIGN_AND_CALL_MT.out.txt              // channel: [ val(meta), path(txt) ]
+        html           = ALIGN_AND_CALL_MT.out.html             // channel: [ val(meta), path(html) ]
+        txt_sh         = ALIGN_AND_CALL_MT_SHIFT.out.txt        // channel: [ val(meta), path(txt) ]
+        html_sh        = ALIGN_AND_CALL_MT_SHIFT.out.html       // channel: [ val(meta), path(html) ]
+        versions       = ch_versions                            // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/mitochondria/align_and_call_MT.nf b/subworkflows/local/mitochondria/align_and_call_MT.nf
@@ -14,6 +14,7 @@ include { GATK4_MUTECT2 as GATK4_MUTECT2_MT                                 } fr
 include { GATK4_FILTERMUTECTCALLS as  GATK4_FILTERMUTECTCALLS_MT            } from '../../../modules/nf-core/gatk4/filtermutectcalls/main'
 include { TABIX_TABIX as TABIX_TABIX_MT                                     } from '../../../modules/nf-core/tabix/tabix/main'
 include { MT_DELETION                                                       } from '../../../modules/local/mt_deletion_script'
+include { EKLIPSE as EKLIPSE_MT                                             } from '../../../modules/nf-core/eklipse/main'
 
 workflow ALIGN_AND_CALL_MT {
     take:
@@ -50,6 +51,8 @@ workflow ALIGN_AND_CALL_MT {
         ch_sort_index_bam        = SAMTOOLS_SORT_MT.out.bam.join(SAMTOOLS_INDEX_MT.out.bai, failOnMismatch:true, failOnDuplicate:true)
         ch_sort_index_bam_int_mt = ch_sort_index_bam.combine(ch_intervals)
 
+        EKLIPSE_MT(ch_sort_index_bam,[])
+
         MT_DELETION(ch_sort_index_bam, ch_fasta)
 
         GATK4_MUTECT2_MT (ch_sort_index_bam_int_mt, ch_fasta, ch_fai, ch_dict, [], [], [],[])
@@ -72,18 +75,22 @@ workflow ALIGN_AND_CALL_MT {
         ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions.first())
         ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions.first())
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MT.out.versions.first())
+        ch_versions = ch_versions.mix(EKLIPSE_MT.out.versions.first())
         ch_versions = ch_versions.mix(MT_DELETION.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_MUTECT2_MT.out.versions.first())
         ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_FILTERMUTECTCALLS_MT.out.versions.first())
 
     emit:
-        vcf           = GATK4_FILTERMUTECTCALLS_MT.out.vcf   // channel: [ val(meta), path(vcf) ]
-        tbi           = GATK4_FILTERMUTECTCALLS_MT.out.tbi   // channel: [ val(meta), path(tbi) ]
-        stats         = GATK4_MUTECT2_MT.out.stats           // channel: [ val(meta), path(stats) ]
-        filt_stats    = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ]
-        txt           = HAPLOCHECK_MT.out.txt                // channel: [ val(meta), path(txt) ]
-        html          = HAPLOCHECK_MT.out.html               // channel: [ val(meta), path(html) ]
-        mt_del_result = MT_DELETION.out.mt_del_result        // channel: [ val(meta), path(txt) ]
-        versions      = ch_versions                          // channel: [ path(versions.yml) ]
+        vcf            = GATK4_FILTERMUTECTCALLS_MT.out.vcf   // channel: [ val(meta), path(vcf) ]
+        tbi            = GATK4_FILTERMUTECTCALLS_MT.out.tbi   // channel: [ val(meta), path(tbi) ]
+        stats          = GATK4_MUTECT2_MT.out.stats           // channel: [ val(meta), path(stats) ]
+        filt_stats     = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ]
+        eklipse_del    = EKLIPSE_MT.out.deletions             // channel: [ val(meta), path(csv) ]
+        eklipse_genes  = EKLIPSE_MT.out.genes                 // channel: [ val(meta), path(csv) ]
+        eklipse_circos = EKLIPSE_MT.out.circos                // channel: [ val(meta), path(png) ]
+        txt            = HAPLOCHECK_MT.out.txt                // channel: [ val(meta), path(txt) ]
+        html           = HAPLOCHECK_MT.out.html               // channel: [ val(meta), path(html) ]
+        mt_del_result  = MT_DELETION.out.mt_del_result        // channel: [ val(meta), path(txt) ]
+        versions       = ch_versions                          // channel: [ path(versions.yml) ]
 }