Merge pull request #645 from maxulysse/dev_CI

merge tests/nextflow.config in conf/test.config
nf-core · Jul 17, 2022 · 9683205 · 9683205
2 parents 28aa979 + fcd2636
commit 9683205
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -89,6 +89,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
 - [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
 - [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
+- [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
 
 ### Fixed
 

diff --git a/conf/test.config b/conf/test.config
@@ -195,3 +195,37 @@ profiles {
         params.input               = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv"
     }
 }
+
+process {
+    withName:'FREEC_SOMATIC'{
+        ext.args = {
+            [
+                "sample":[
+                    inputformat: 'pileup',
+                    mateorientation: 'FR'
+                ],
+                "general" :[
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                    ],
+                "control":[
+                    inputformat: "pileup",
+                    mateorientation: "FR"
+                ]
+            ]
+        }
+    }
+
+    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
+        //sample name from when the test data was generated
+        ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
+    }
+
+    withName: 'FILTERVARIANTTRANCHES'{
+        ext.args         = { "--info-key CNN_1D --indel-tranche 0" }
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml
@@ -1,5 +1,5 @@
 - name: Run alignment to fastq and then remap on bam files
-  command: nextflow run main.nf -profile test,alignment_to_fastq,docker -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,alignment_to_fastq,docker
   tags:
     - alignment_to_fastq
 

diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml
@@ -1,5 +1,5 @@
 - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit -c ./tests/nextflow.config  --only_paired_variant_calling
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit --only_paired_variant_calling
   tags:
     - cnvkit
     - somatic

diff --git a/tests/test_tools.yml b/tests/test_tools.yml
@@ -1,5 +1,5 @@
 - name: Run variant calling on somatic samples with cnvkit
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit
   tags:
     - cnvkit
     - somatic
@@ -32,7 +32,7 @@
     - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on tumor_only sample with cnvkit
-  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit
   tags:
     - cnvkit
     - tumor_only
@@ -51,7 +51,7 @@
     - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on germline sample with cnvkit
-  command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit
   tags:
     - cnvkit
     - germline
@@ -71,7 +71,7 @@
     - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on somatic samples with controlfreec
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec
   tags:
     - controlfreec
     - somatic
@@ -96,7 +96,7 @@
     - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
 
 - name: Run variant calling on somatic samples with controlfreec without intervals
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec -c ./tests/nextflow.config --no_intervals -stub-run
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec --no_intervals -stub-run
   tags:
     - controlfreec
     - no_intervals
@@ -239,7 +239,7 @@
 #     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller
-  command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  -c ./tests/nextflow.config --step variant_calling
+  command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  --step variant_calling
   tags:
     - germline
     - haplotypecaller
@@ -256,7 +256,7 @@
     - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller without intervals
-  command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  -c ./tests/nextflow.config --step variant_calling --no_intervals
+  command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  --step variant_calling --no_intervals
   tags:
     - germline
     - haplotypecaller
@@ -274,7 +274,7 @@
     - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 # - name: Run joint germline variant calling with haplotypecaller
-#   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline -c ./tests/nextflow.config
+#   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline
 #   tags:
 #     - germline
 #     - gvcf
@@ -288,7 +288,7 @@
 #     - path: results/csv/variantcalled.csv
 
 # - name: Run joint germline variant calling with haplotypecaller without intervals
-#   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline --no_intervals -c ./tests/nextflow.config
+#   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline --no_intervals
 #   tags:
 #     - germline
 #     - gvcf
@@ -448,7 +448,7 @@
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with mutect2
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2
   tags:
     - mutect2_manual
     - manual
@@ -617,7 +617,7 @@
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with tiddit
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools tiddit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools tiddit
   tags:
     - tiddit
     - somatic
@@ -634,7 +634,7 @@
     - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.ploidies.tab
 
 - name: Run variant calling on germline sample with tiddit
-  command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit
   tags:
     - tiddit
     - germline
@@ -645,7 +645,7 @@
     - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with tiddit
-  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit -c ./tests/nextflow.config
+  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit
   tags:
     - tiddit
     - tumor_only