Merge branch 'rework-tests' into newmain

.gitlab-ci.yml

@@ -27,7 +27,7 @@ test-python:
 
 
 test-docker-compose:
-  image: docker/compose
+  image: docker:24
   needs: []
   # when: delayed
   # start_in: 3 minutes
@@ -37,10 +37,11 @@ test-docker-compose:
     when: runner_system_failure
   script:
   - apk update && apk upgrade && apk add jq bash curl
+  - docker compose version
   - ./test_docker_compose.sh
   after_script:
-    - docker-compose logs back > log/docker-compose.back.log
-    - docker-compose logs > log/docker-compose.log
+    - docker compose logs back > log/docker-compose.back.log
+    - docker compose logs > log/docker-compose.log
   artifacts:
     when: always
     paths:

jass/test/data_test1/COV.csv

-ID	z_DISNEY_RATATOUY	z_DISNEY_POCAHONT
-z_DISNEY_RATATOUY	2.05403006060606	0.394332909090909
-z_DISNEY_POCAHONT	0.394332909090909	1.17729254545455

jass/test/data_test1/SumStatTab.txt

-rsid	position	chr	region	Z_ratatouy	Z_pocahont
-rs1	1	1	1	0.812	-1.06
-rs2	2	1	1	2.197	0.937
-rs3	3	1	2	2.049	0.854
-rs4	1	2	3	1.632	1.461
-rs5	2	2	3	0.254	-1.413
-rs6	3	2	4	0.491	0.567
-rs7	4	2	4	-0.324	0.583
-rs8	5	2	4	-1.662	-1.307
-rs9	1	3	5	1.768	-0.54
-rs10	2	3	5	0.026	1.948
-rs11	3	3	6	1.129	0.054
-rs12	4	3	7	-2.38	0.352

jass/test/data_test1/metadata.txt

-information	content
-title	Mock dataset with disney
-description	"lorem ipsum"
-ancestry	DIS
-assembly	dSNY

jass/test/data_test1/regions.txt

-chr	start	stop
-chr1	1	2
-chr1	3	4
-chr2	1	2
-chr2	3	5
-chr3	1	2
-chr3	3	3
-chr3	4	4

jass/test/data_test1/summary.csv

-Outcome	FullName	Consortium	Type	Reference	ReferenceLink	dataLink	internalDataLink	Nsample	Ncase	Ncontrol
-RATATOUY	Ratatouille ou la mort de l'hygiène en cuisine	DISNEY	BrainWashing	Courgette et al., 1754	http://www.marmiton.org/recettes/recette_ratatouille_23223.asp	pouet	pouet	1000000		
-POCAHONT	Pocahontas mange des tapas	DISNEY	BrainWashing	Rolfe et al., 1614	https://fr.wikipedia.org/wiki/Pocahontas	Gargar	Gargar	1000000		

jass/test/data_test1/z_DISNEY_POCAHONT_chr1.txt

-rsid	position	refAllele	altAllele	Z
-rs1	1	C	T	-1.06
-rs2	2	G	T	0.937
-rs3	3	C	T	0.854

jass/test/data_test1/z_DISNEY_POCAHONT_chr2.txt

-rsid	position	refAllele	altAllele	Z
-rs4	1	G	T	1.461
-rs5	2	A	T	-1.413
-rs6	3	A	C	0.567
-rs7	4	A	G	0.583
-rs8	5	C	G	-1.307

jass/test/data_test1/z_DISNEY_POCAHONT_chr3.txt

-rsid	position	refAllele	altAllele	Z
-rs9	1	C	T	-0.54
-rs10	2	G	T	1.948
-rs11	3	A	C	0.054
-rs12	4	A	C	0.352

jass/test/data_test1/z_DISNEY_RATATOUY_chr1.txt

-rsid	position	refAllele	altAllele	Z
-rs1	1	C	T	0.812
-rs2	2	G	T	2.197
-rs3	3	C	T	2.049

jass/test/data_test1/z_DISNEY_RATATOUY_chr2.txt

-rsid	position	refAllele	altAllele	Z
-rs4	1	G	T	1.632
-rs5	2	A	T	0.254
-rs6	3	A	C	0.491
-rs7	4	A	G	-0.324
-rs8	5	C	G	-1.662

jass/test/data_test1/z_DISNEY_RATATOUY_chr3.txt

-rsid	position	refAllele	altAllele	Z
-rs9	1	C	T	1.768
-rs10	2	G	T	0.026
-rs11	3	A	C	1.129
-rs12	4	A	C	-2.38

jass/test/data_test2/COV.csv

-ID	z_BMW_ISETTA	z_BMW_MINI	z_FIAT_CINQCENT	z_FIAT_CINQUECENTO	z_MERCO_SMART	z_TATA_TATANANO
-z_BMW_ISETTA	2	1	1	1	1	1
-z_BMW_MINI	1	2	1	1	1	1
-z_FIAT_CINQCENT	1	1	2	1	1	1
-z_FIAT_CINQUECENTO	1	1	1	2	1	1
-z_MERCO_SMART	1	1	1	1	2	1
-z_TATA_TATANANO	1	1	1	1	1	2