diff --git a/CHANGELOG.md b/CHANGELOG.md index 2583ba67..fe003c06 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/README.md b/README.md index a049c1a4..7e2fb3a9 100644 --- a/README.md +++ b/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 diff --git a/tests/csv/panel.csv b/tests/csv/panel.csv index b7b37f1a..91f70d1d 100644 --- a/tests/csv/panel.csv +++ b/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 diff --git a/tests/csv/sample_bam.csv b/tests/csv/sample_bam.csv index b128cac0..78269414 100644 --- a/tests/csv/sample_bam.csv +++ b/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 diff --git a/tests/csv/sample_vcf.csv b/tests/csv/sample_vcf.csv index 01b504e5..14558dc1 100644 --- a/tests/csv/sample_vcf.csv +++ b/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