Merge pull request #800 from bigbio/fix-hyperlink-inconsistency

ypriverol · web-flow · commit 56415244701c · 2026-02-22T21:19:22.000Z
Fix hyperlink inconsistency
diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
 # Proteomics Sample Metadata Format
 
 [![Version](https://flat.badgen.net/static/sdrf-proteomics/1.0.1/orange)](CHANGELOG.md)
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+[![License](https://flat.badgen.net/github/license/bigbio/proteomics-sample-metadata)](https://github.com/bigbio/proteomics-sample-metadata/blob/master/LICENSE)
+[![Open Issues](https://flat.badgen.net/github/open-issues/bigbio/proteomics-sample-metadata)](https://github.com/bigbio/proteomics-sample-metadata/issues)
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 ## Improving metadata annotation of Proteomics datasets
@@ -45,7 +45,7 @@ In the [annotated projects](https://github.com/bigbio/proteomics-metadata-standa
 Annotate a dataset in 5 steps:
 
 - Read the [SDRF-Proteomics specification](https://github.com/bigbio/proteomics-metadata-standard/tree/master/sdrf-proteomics).
-- Depending on the type of dataset, choose the appropriate [sample template](https://github.com/bigbio/proteomics-metadata-standard/tree/master/sdrf-proteomics#sdrf-templates).
+- Depending on the type of dataset, choose the appropriate [sample template](https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#sdrf-templates).
 - Annotate the corresponding ProteomeXchange PXD dataset following the guidelines.
 - Validate your SDRF file:
 
diff --git a/sdrf-proteomics/VERSIONING.adoc b/sdrf-proteomics/VERSIONING.adoc
@@ -504,6 +504,6 @@ When a breaking change is introduced, a migration guide MUST be provided. The gu
 
 * link:README.adoc[SDRF-Proteomics Core Specification] — see <<versioning>> section
 * link:metadata-guidelines/template-definitions.adoc[Template Definitions Guide] — YAML schema structure
-* link:open-issues.adoc[Open Issues and Future Decisions] — active community discussions
+* https://github.com/bigbio/proteomics-sample-metadata/issues[Open Issues and Future Decisions] — active community discussions
 * https://semver.org/[Semantic Versioning 2.0.0]
 * https://github.com/bigbio/proteomics-sample-metadata/issues/771[Issue #771: Versioning strategy discussion]
diff --git a/sdrf-proteomics/templates/affinity-proteomics/README.adoc b/sdrf-proteomics/templates/affinity-proteomics/README.adoc
@@ -581,7 +581,7 @@ NOTE: MS-specific validations (label, cleavage agent, etc.) do not apply to affi
 
 The affinity proteomics SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/affinity-proteomics/1.1.0/affinity-proteomics.sdrf.tsv[affinity-proteomics.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/affinity-proteomics/1.1.0/affinity-proteomics.sdrf.tsv[affinity-proteomics.sdrf.tsv]
 
 [[related-templates]]
 == Related Templates
diff --git a/sdrf-proteomics/templates/base/README.adoc b/sdrf-proteomics/templates/base/README.adoc
@@ -28,5 +28,5 @@ Use one of the following technology templates instead:
 [[files]]
 == Template Files
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/base/1.1.0/base.yaml[base.yaml] - YAML template definition for validation
-- link:https://github.com/bigbio/sdrf-templates/blob/master/base/1.1.0/base.sdrf.tsv[base.sdrf.tsv] - Column header template
+- link:https://github.com/bigbio/sdrf-templates/blob/main/base/1.1.0/base.yaml[base.yaml] - YAML template definition for validation
+- link:https://github.com/bigbio/sdrf-templates/blob/main/base/1.1.0/base.sdrf.tsv[base.sdrf.tsv] - Column header template
diff --git a/sdrf-proteomics/templates/cell-lines/README.adoc b/sdrf-proteomics/templates/cell-lines/README.adoc
@@ -584,7 +584,7 @@ For cell lines where donor information is unknown:
 
 The cell line SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/cell-lines/1.1.0/cell-lines.sdrf.tsv[cell-lines.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/cell-lines/1.1.0/cell-lines.sdrf.tsv[cell-lines.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/crosslinking/README.adoc b/sdrf-proteomics/templates/crosslinking/README.adoc
@@ -493,6 +493,13 @@ parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv \
   --template crosslinking
 ----
 
+[[template-file]]
+== Template File
+
+The crosslinking SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/crosslinking/1.1.0/crosslinking.sdrf.tsv[crosslinking.sdrf.tsv]
+
 [[references]]
 == References
 
diff --git a/sdrf-proteomics/templates/dda-acquisition/README.adoc b/sdrf-proteomics/templates/dda-acquisition/README.adoc
@@ -356,7 +356,7 @@ NOTE: For TMT experiments, multiple samples share the same raw file. Use `commen
 
 The DDA SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/dda-acquisition/1.1.0/dda-acquisition.sdrf.tsv[dda-acquisition.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/dda-acquisition/1.1.0/dda-acquisition.sdrf.tsv[dda-acquisition.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/dia-acquisition/README.adoc b/sdrf-proteomics/templates/dia-acquisition/README.adoc
@@ -419,7 +419,7 @@ For ion mobility-enhanced DIA (diaPASEF), additional columns may be relevant:
 
 The DIA SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/dia-acquisition/1.1.0/dia-acquisition.sdrf.tsv[dia-acquisition.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/dia-acquisition/1.1.0/dia-acquisition.sdrf.tsv[dia-acquisition.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/human/README.adoc b/sdrf-proteomics/templates/human/README.adoc
@@ -1655,3 +1655,10 @@ For female patients. Values: `pre-menopausal`, `peri-menopausal`, `post-menopaus
 === Staging Systems
 - TNM Classification: AJCC Cancer Staging Manual
 - Ann Arbor Staging: Lymphoma staging system
+
+[[template-file]]
+== Template File
+
+The human SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/human/1.1.0/human.sdrf.tsv[human.sdrf.tsv]
diff --git a/sdrf-proteomics/templates/immunopeptidomics/README.adoc b/sdrf-proteomics/templates/immunopeptidomics/README.adoc
@@ -286,7 +286,7 @@ Examples of immunopeptidomics datasets annotated with SDRF-Proteomics:
 
 The immunopeptidomics SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/immunopeptidomics/1.0.0-dev/immunopeptidomics.sdrf.tsv[immunopeptidomics.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/immunopeptidomics/1.0.0-dev/immunopeptidomics.sdrf.tsv[immunopeptidomics.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/invertebrates/README.adoc b/sdrf-proteomics/templates/invertebrates/README.adoc
@@ -200,6 +200,13 @@ pip install sdrf-pipelines
 sdrf_validate --sdrf_file your_file.sdrf.tsv --template invertebrates
 ----
 
+[[template-file]]
+== Template File
+
+The invertebrates SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/invertebrates/1.1.0/invertebrates.sdrf.tsv[invertebrates.sdrf.tsv]
+
 [[examples]]
 == Examples
 
diff --git a/sdrf-proteomics/templates/metaproteomics/README.adoc b/sdrf-proteomics/templates/metaproteomics/README.adoc
@@ -507,7 +507,7 @@ For metaproteomics, consider documenting:
 
 The metaproteomics SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/metaproteomics/1.0.0-dev/metaproteomics.sdrf.tsv[metaproteomics.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/metaproteomics/1.0.0-dev/metaproteomics.sdrf.tsv[metaproteomics.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/ms-proteomics/README.adoc b/sdrf-proteomics/templates/ms-proteomics/README.adoc
@@ -473,6 +473,13 @@ endif::[]
 * link:../dia-acquisition/README.adoc[DIA Acquisition] - DIA-specific columns
 * link:../human/README.adoc[Human Template] - Human sample metadata
 
+[[template-file]]
+== Template File
+
+The MS-Proteomics SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/ms-proteomics/1.1.0/ms-proteomics.sdrf.tsv[ms-proteomics.sdrf.tsv]
+
 == Ontologies
 
 - PRIDE Ontology: https://www.ebi.ac.uk/ols4/ontologies/pride
diff --git a/sdrf-proteomics/templates/olink/README.adoc b/sdrf-proteomics/templates/olink/README.adoc
@@ -289,7 +289,7 @@ parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv --template olink
 
 The Olink SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/olink/1.0.0/olink.sdrf.tsv[olink.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/olink/1.0.0/olink.sdrf.tsv[olink.sdrf.tsv]
 
 [[related-templates]]
 == Related Templates
diff --git a/sdrf-proteomics/templates/plants/README.adoc b/sdrf-proteomics/templates/plants/README.adoc
@@ -208,6 +208,13 @@ pip install sdrf-pipelines
 sdrf_validate --sdrf_file your_file.sdrf.tsv --template plants
 ----
 
+[[template-file]]
+== Template File
+
+The plants SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/plants/1.1.0/plants.sdrf.tsv[plants.sdrf.tsv]
+
 [[examples]]
 == Examples
 
diff --git a/sdrf-proteomics/templates/single-cell/README.adoc b/sdrf-proteomics/templates/single-cell/README.adoc
@@ -553,7 +553,7 @@ Following the Nature Methods SCP guidelines:
 
 The single cell proteomics SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/single-cell/1.0.0/single-cell.sdrf.tsv[single-cell.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/single-cell/1.0.0/single-cell.sdrf.tsv[single-cell.sdrf.tsv]
 
 [[validation]]
 == Validation
diff --git a/sdrf-proteomics/templates/somascan/README.adoc b/sdrf-proteomics/templates/somascan/README.adoc
@@ -320,7 +320,7 @@ parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv --template somascan
 
 The SomaScan SDRF template file is available in the sdrf-templates repository:
 
-- link:https://github.com/bigbio/sdrf-templates/blob/master/somascan/1.0.0/somascan.sdrf.tsv[somascan.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/somascan/1.0.0/somascan.sdrf.tsv[somascan.sdrf.tsv]
 
 [[related-templates]]
 == Related Templates
diff --git a/sdrf-proteomics/templates/vertebrates/README.adoc b/sdrf-proteomics/templates/vertebrates/README.adoc
@@ -154,6 +154,13 @@ pip install sdrf-pipelines
 sdrf_validate --sdrf_file your_file.sdrf.tsv --template vertebrates
 ----
 
+[[template-file]]
+== Template File
+
+The vertebrates SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/vertebrates/1.1.0/vertebrates.sdrf.tsv[vertebrates.sdrf.tsv]
+
 [[examples]]
 == Examples
 
