Merge pull request #345 from fellen31/add-metro-map

Add metro map
genomic-medicine-sweden · Aug 30, 2024 · 87c67ef · 87c67ef
2 parents a7d1879 + 16c4139
commit 87c67ef
Show file tree

Hide file tree

Showing 13 changed files with 2,801 additions and 71 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -59,6 +59,7 @@ jobs:
         tags:
           - "SHORT_VARIANT_CALLING"
           - "SNV_ANNOTATION"
+          - "CALL_SVS"
           - "samplesheet"
           - "samplesheet_multisample_bam"
         profile:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,9 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#345](https://github.com/genomic-medicine-sweden/nallo/pull/345) - Added first version of a metro map
+- [#346](https://github.com/genomic-medicine-sweden/nallo/pull/#346) - Added nf-test to call_svs
+
 ### `Changed`
 
 - [#344](https://github.com/genomic-medicine-sweden/nallo/pull/344) - Changed version to 0.4.0dev
+- [#346](https://github.com/genomic-medicine-sweden/nallo/pull/346) - Renamed structural_variant_calling to call_svs
 
 ### `Removed`
 

diff --git a/README.md b/README.md
@@ -14,6 +14,10 @@
 
 ## Pipeline summary
 
+<picture align="center">
+    <img alt="genomic-medicine-sweden/nallo workflow" src="docs/images/nallo_metromap.png">
+  </picture>
+
 ##### QC
 
 - FastQC ([`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))

diff --git a/...modules/structural_variant_calling.config → conf/modules/call_svs.config b/...modules/structural_variant_calling.config → conf/modules/call_svs.config
@@ -14,27 +14,22 @@ process {
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Structural variant calling
+    Call SVs
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    withName: '.*:STRUCTURAL_VARIANT_CALLING:SNIFFLES' {
-
+    withName: '.*:CALL_SVS:SNIFFLES' {
         ext.prefix = { "${meta.id}_sniffles" }
-
         ext.args = '--no-qc'
-
         publishDir = [
             path: { "${params.outdir}/sv_calling/sniffles/single_sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*:STRUCTURAL_VARIANT_CALLING:SNIFFLES_MULTISAMPLE' {
-
+    withName: '.*:CALL_SVS:SNIFFLES_MULTISAMPLE' {
         ext.prefix = { "${meta.id}_sniffles" }
-
         publishDir = [
             path: { "${params.outdir}/sv_calling/sniffles/multi_sample/${meta.id}" },
             mode: params.publish_dir_mode,

diff --git a/docs/images/nallo_metromap.png b/docs/images/nallo_metromap.png
diff --git a/modules.json b/modules.json
@@ -203,7 +203,8 @@
                     "sniffles": {
                         "branch": "master",
                         "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/sniffles/sniffles.diff"
                     },
                     "somalier/extract": {
                         "branch": "master",

diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf
diff --git a/modules/nf-core/sniffles/sniffles.diff b/modules/nf-core/sniffles/sniffles.diff
diff --git a/nextflow.config b/nextflow.config
@@ -312,7 +312,7 @@ includeConfig 'conf/modules/scatter_genome.config'
 includeConfig 'conf/modules/rank_variants.config'
 includeConfig 'conf/modules/short_variant_calling.config'
 includeConfig 'conf/modules/snv_annotation.config'
-includeConfig 'conf/modules/structural_variant_calling.config'
+includeConfig 'conf/modules/call_svs.config'
 includeConfig 'conf/modules/short_variant_calling.config'
 includeConfig 'conf/modules/cnv.config'
 

diff --git a/...flows/local/structural_variant_calling.nf → subworkflows/local/call_svs/main.nf b/...flows/local/structural_variant_calling.nf → subworkflows/local/call_svs/main.nf
@@ -1,13 +1,13 @@
-include { SNIFFLES as SNIFFLES_MULTISAMPLE } from '../../modules/nf-core/sniffles/main'
-include { SNIFFLES                         } from '../../modules/nf-core/sniffles/main'
+include { SNIFFLES as SNIFFLES_MULTISAMPLE } from '../../../modules/nf-core/sniffles/main'
+include { SNIFFLES                         } from '../../../modules/nf-core/sniffles/main'
 
-workflow STRUCTURAL_VARIANT_CALLING {
+workflow CALL_SVS {
 
     take:
-    ch_bam_bai // channel: [ val(meta), [[ bam ], [bai]] ]
-    ch_fasta
-    ch_fai
-    ch_tandem_repeats
+    ch_bam_bai        // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
+    ch_fasta          // channel: [mandatory] [ val(meta), path(fasta) ]
+    ch_fai            // channel: [mandatory] [ val(meta), path(fai) ]
+    ch_tandem_repeats // channel: [optional]  [ val(meta), path(bed) ]
 
     main:
     ch_versions     = Channel.empty()
@@ -26,8 +26,8 @@ workflow STRUCTURAL_VARIANT_CALLING {
     ch_versions = ch_versions.mix(SNIFFLES_MULTISAMPLE.out.versions)
 
     emit:
-    ch_sv_calls_vcf = SNIFFLES.out.vcf             // channel: [ val(meta), vcf]
-    ch_multisample  = SNIFFLES_MULTISAMPLE.out.vcf // channel: [ val(meta), multisample.sniffles.vcf ]
-    versions        = ch_versions                  // channel: [ versions.yml ]
+    ch_sv_calls_vcf = SNIFFLES.out.vcf             // channel: [ val(meta), path(vcf) ]
+    ch_multisample  = SNIFFLES_MULTISAMPLE.out.vcf // channel: [ val(meta), path(vcf) ]
+    versions        = ch_versions                  // channel: [ path(versions.yml) ]
 }