From 19a98f9fa75ea2da0ec1cdd43cde11dc671b7ecd Mon Sep 17 00:00:00 2001 From: Eugenia Fontecha Date: Tue, 19 Mar 2024 14:41:07 +0000 Subject: [PATCH 1/3] change csv files to point to the nf-core repository --- tests/csv/panel.csv | 2 +- tests/csv/sample_bam.csv | 6 +++--- tests/csv/sample_vcf.csv | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/csv/panel.csv b/tests/csv/panel.csv index b7b37f1a..b78d677b 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/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf.csi,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.sites.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/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..05970e33 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/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam.bai +NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam.bai +NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/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..856af18d 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/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf.csi +NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf.csi +NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bcf.csi From 1bc6ad2f9aad8c17b64904a776bfc2704f88b21e Mon Sep 17 00:00:00 2001 From: Eugenia Fontecha Date: Tue, 19 Mar 2024 15:01:41 +0000 Subject: [PATCH 2/3] fix github urls in csv files --- tests/csv/panel.csv | 2 +- tests/csv/sample_bam.csv | 6 +++--- tests/csv/sample_vcf.csv | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/csv/panel.csv b/tests/csv/panel.csv index b78d677b..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/nf-core/test-datasets/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf.csi,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.sites.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/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 05970e33..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/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bam.bai -NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bam.bai -NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/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 856af18d..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/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf.csi -NA19401,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf.csi -NA20359,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/data/individuals/NA20359/NA20359.s.1x.bcf,https://raw.githubusercontent.com/nf-core/test-datasets/blob/phaseimpute/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 From 7a1cabee381a910c0ffd8f9e93b42a2629002a98 Mon Sep 17 00:00:00 2001 From: Eugenia Fontecha Date: Tue, 19 Mar 2024 15:48:57 +0000 Subject: [PATCH 3/3] prettify CHAGELOG file --- CHANGELOG.md | 4 ++++ README.md | 1 + 2 files changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6ef061e9..fbf7c369 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,10 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co ### `Added` +### `Changed` + +[#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository + ### `Fixed` ### `Dependencies` diff --git a/README.md b/README.md index bc0384fb..a94eb7a4 100644 --- a/README.md +++ b/README.md @@ -92,6 +92,7 @@ We thank the following people for their extensive assistance in the development - Anabella Trigilla - Saul Pierotti +- Eugenia Fontecha ## Contributions and Support