Merge pull request #15 from eugeniafontecha/dev

Csv files point to nf-core repository

CHANGELOG.md

@@ -11,6 +11,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 
 ### `Changed`
 
+- [#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository
 - [#16](https://github.com/nf-core/phaseimpute/pull/16) - Removed outdir from test config files
 
 ### `Fixed`

README.md

@@ -92,6 +92,7 @@ We thank the following people for their extensive assistance in the development
 
 - Anabella Trigila
 - Saul Pierotti
+- Eugenia Fontecha
 - Matias Romero Victorica
 
 ## Contributions and Support

tests/csv/panel.csv

@@ -1,2 +1,2 @@
 panel,vcf,index,sites,tsv,legend,phased
-1000GP.s.norel,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/panel/21_22/1000GP.chr21_22.s.norel.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/panel/21_22/1000GP.chr21_22.s.norel.bcf.csi,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/panel/21_22/1000GP.chr21_22.s.norel.sites.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/panel/21_22/1000GP.chr21_22.s.norel.tsv.gz,,TRUE
+1000GP.s.norel,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf.csi,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.sites.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.tsv.gz,,TRUE

tests/csv/sample_bam.csv

@@ -1,4 +1,4 @@
 sample,bam,bai
-NA12878,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bam,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bam.bai
-NA19401,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bam,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bam.bai
-NA20359,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bam,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bam.bai
+NA12878,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam.bai
+NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam.bai
+NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bam.bai

tests/csv/sample_vcf.csv

@@ -1,4 +1,4 @@
 sample,vcf,csi
-NA12878,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bcf.csi
-NA19401,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bcf.csi
-NA20359,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bcf.csi
+NA12878,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf.csi
+NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf.csi
+NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bcf.csi