Changed test_tools, updated ci.yaml, removed mpileup from pair_varcal…

…ling, fixed space in germline_varcalling, updated subway map (text was slightly changed by inkscape automatically), updated Changelog

.github/workflows/ci.yml

@@ -42,6 +42,7 @@ jobs:
           - "haplotypecaller"
           - "manta"
           - "markduplicates"
+          - "mpileup"
           - "msisensorpro"
           - "mutect2"
           - "prepare_recalibration"

CHANGELOG.md

@@ -32,7 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
 
 ### Changed
-
+- [#570](https://github.com/nf-core/sarek/pull/570) - Extract mpileup into its own subworkflow; zip mpileup files
 - [#383](https://github.com/nf-core/sarek/pull/383), [#528](https://github.com/nf-core/sarek/pull/528) - Update `CHANGELOG`
 - [#390](https://github.com/nf-core/sarek/pull/390) - Update `nextflow_schema.json`
 - [#408](https://github.com/nf-core/sarek/pull/408) - Sync `TEMPLATE` with `tools` `2.0.1`

subworkflows/local/germline_variant_calling.nf

@@ -40,7 +40,7 @@ workflow GERMLINE_VARIANT_CALLING {
     manta_vcf           = Channel.empty()
     strelka_vcf         = Channel.empty()
     tiddit_vcf          = Channel.empty()
-    mpileup              = Channel.empty()
+    mpileup             = Channel.empty()
 
     // Remap channel with intervals
     cram_recalibrated_intervals = cram_recalibrated.combine(intervals)

subworkflows/local/pair_variant_calling.nf

@@ -65,7 +65,7 @@ workflow PAIR_VARIANT_CALLING {
 
         }
 
-    if (tools.contains('mpileup') || tools.contains('controlfreec')){
+    if (tools.contains('controlfreec')){
         cram_normal_intervals_no_index = cram_pair_intervals
                     .map {meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
                             [meta, normal_cram, intervals]
@@ -79,9 +79,7 @@ workflow PAIR_VARIANT_CALLING {
         mpileup_normal = RUN_MPILEUP_NORMAL.out.mpileup
         RUN_MPILEUP_TUMOR(cram_tumor_intervals_no_index, fasta)
         mpileup_tumor = RUN_MPILEUP_TUMOR.out.mpileup
-    }
 
-    if (tools.contains('controlfreec')){
         controlfreec_input = mpileup_normal.cross(mpileup_tumor)
         .map{ normal, tumor ->
             [normal[0], normal[1], tumor[1], [], [], [], []]

tests/test_tools.yml

@@ -603,28 +603,36 @@
     - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
-- name: Run variant calling on somatic sample to test mpileup
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mpileup
+- name: Run variant calling on tumor_only sample to test mpileup
+  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup
   tags:
-    - somatic
+    - tumor_only
     - mpileup
   files:
-    - path: results/variant_calling/sample3/mpileup/sample3.normal.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.normal.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.tumor.mpileup.gz
+    - path: results/variant_calling/sample2/mpileup/sample2.tumor.mpileup.gz
 
-- name: Run variant calling on tumor_only sample to test mpileup
-  command: nextflow run main.nf -profile test,tumor_only,docker --tools mpileup
+- name: Run variant calling on tumor_only sample to test mpileup without intervals
+  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup --no_intervals
   tags:
     - tumor_only
     - mpileup
+    - no_intervals
   files:
     - path: results/variant_calling/sample2/mpileup/sample2.tumor.mpileup.gz
 
 - name: Run variant calling on germline sample to test mpileup
   command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup
   tags:
-    - tumor_only
+    - germline
+    - mpileup
+  files:
+    - path: results/variant_calling/sample1/mpileup/sample1.normal.mpileup.gz
+
+- name: Run variant calling on germline sample to test mpileup without intervals
+  command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup --no_intervals
+  tags:
+    - germline
     - mpileup
+    - no_intervals
   files:
     - path: results/variant_calling/sample1/mpileup/sample1.normal.mpileup.gz