Merge pull request #189 from MaxUlysse/Freebayes

fix no_intervals for HaplotypeCaller

.github/workflows/ci.yml

@@ -122,7 +122,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tool: [Haplotypecaller, Freebayes, Manta, mpileup, Strelka, TIDDIT, MSIsensor]
+        tool: [Haplotypecaller, Freebayes, Manta, mpileup, MSIsensor, Strelka, TIDDIT]
+        intervals: [--no_intervals, '']
+        exclude:
+          - tool: Manta
+            intervals: --no_intervals
+          - tool: MSIsensor
+            intervals: --no_intervals
+          - tool: Strelka
+            intervals: --no_intervals
+          - tool: TIDDIT
+            intervals: --no_intervals
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
@@ -135,4 +145,4 @@ jobs:
       - name: Pull docker image
         run: docker pull nfcore/sarek:dev
       - name: Run ${{ matrix.tool }} test
-        run: nextflow run . -profile test_tool,docker --tools ${{ matrix.tool }}
+        run: nextflow run . -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}

CHANGELOG.md

@@ -81,6 +81,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
 - [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation to fix [#166](https://github.com/nf-core/sarek/issues/166)
 - [#188](https://github.com/nf-core/sarek/pull/188) - Fix input/output channels for process `IndexBamFile` to match actual files in the `mapped.tsv` files
+- [#189](https://github.com/nf-core/sarek/pull/189) - Fix `no_intervals` for process `HaplotypeCaller` (the file just need to actually exists...)
 
 ### Deprecated - [2.6dev]
 

main.nf

@@ -898,7 +898,10 @@ bedIntervals = bedIntervals
 
 bedIntervals = bedIntervals.dump(tag:'bedintervals')
 
-if (params.no_intervals && step != 'annotate') bedIntervals = Channel.from(file("no_intervals.bed"))
+if (params.no_intervals && step != 'annotate') {
+    file("${params.outdir}/no_intervals.bed").text = "no_intervals\n"
+    bedIntervals = Channel.from(file("${params.outdir}/no_intervals.bed"))
+}
 
 (intBaseRecalibrator, intApplyBQSR, intHaplotypeCaller, intFreebayesSingle, intMpileup, bedIntervals) = bedIntervals.into(6)