From 39d365b4330c0b35ee3fbcd713b77d6e864016b5 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Wed, 25 Sep 2024 13:37:13 -0400 Subject: [PATCH 1/5] adjusted relative path --- website/docs/Pipelines/PairedTag_Pipeline/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 0b56dd3847..08999bcf65 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -16,9 +16,9 @@ The [Paired-Tag workflow](https://github.com/broadinstitute/warp/blob/develop/pi The workflow is a wrapper WDL script that calls two subworkflows: the Optimus workflow for single-nucleus GEX data and the ATAC workflow for single-nucleus histone modification data. -The [Optimus workflow](../Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. +The [Optimus workflow](/docs/Pipelines/Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. -The [ATAC workflow](../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. +The [ATAC workflow](../../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. The [wrapper WDL](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/paired_tag/PairedTag.wdl) is available in the [WARP repository](https://github.com/broadinstitute/warp). From 202cd403633a9453afa180e8a0e7d28f51161915 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Wed, 25 Sep 2024 13:41:37 -0400 Subject: [PATCH 2/5] adding relative paths --- website/docs/Pipelines/PairedTag_Pipeline/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 08999bcf65..214937b58f 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -16,7 +16,7 @@ The [Paired-Tag workflow](https://github.com/broadinstitute/warp/blob/develop/pi The workflow is a wrapper WDL script that calls two subworkflows: the Optimus workflow for single-nucleus GEX data and the ATAC workflow for single-nucleus histone modification data. -The [Optimus workflow](/docs/Pipelines/Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. +The [Optimus workflow](../../Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. The [ATAC workflow](../../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. From 32ea908a382908e9ba6ebf1bc4c2d60eb2bf6f8c Mon Sep 17 00:00:00 2001 From: ekiernan Date: Wed, 25 Sep 2024 15:17:33 -0400 Subject: [PATCH 3/5] Revert "adding relative paths" This reverts commit 202cd403633a9453afa180e8a0e7d28f51161915. --- website/docs/Pipelines/PairedTag_Pipeline/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 214937b58f..08999bcf65 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -16,7 +16,7 @@ The [Paired-Tag workflow](https://github.com/broadinstitute/warp/blob/develop/pi The workflow is a wrapper WDL script that calls two subworkflows: the Optimus workflow for single-nucleus GEX data and the ATAC workflow for single-nucleus histone modification data. -The [Optimus workflow](../../Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. +The [Optimus workflow](/docs/Pipelines/Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. The [ATAC workflow](../../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. From 39e4adb761b0175e66b8880fd408a026ba591014 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Wed, 25 Sep 2024 15:17:49 -0400 Subject: [PATCH 4/5] Revert "adjusted relative path" This reverts commit 39d365b4330c0b35ee3fbcd713b77d6e864016b5. --- website/docs/Pipelines/PairedTag_Pipeline/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 08999bcf65..0b56dd3847 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -16,9 +16,9 @@ The [Paired-Tag workflow](https://github.com/broadinstitute/warp/blob/develop/pi The workflow is a wrapper WDL script that calls two subworkflows: the Optimus workflow for single-nucleus GEX data and the ATAC workflow for single-nucleus histone modification data. -The [Optimus workflow](/docs/Pipelines/Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. +The [Optimus workflow](../Optimus_Pipeline/README) (GEX) corrects cell barcodes (CBs) and Unique Molecular Identifiers (UMIs), aligns reads to the genome, calculates per-barcode and per-gene quality metrics, and produces a raw cell-by-gene count matrix. -The [ATAC workflow](../../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. +The [ATAC workflow](../ATAC/README) (histone modification) performs demultiplexing for samples that have a preindex barcode, corrects CBs, aligns reads to the genome, calculates per-barcode quality metrics, and produces a fragment file. The [wrapper WDL](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/paired_tag/PairedTag.wdl) is available in the [WARP repository](https://github.com/broadinstitute/warp). From 38aa6011c28f0a1435710e4e30935dfe7360a6cb Mon Sep 17 00:00:00 2001 From: ekiernan Date: Wed, 25 Sep 2024 15:23:14 -0400 Subject: [PATCH 5/5] adding trailingslash config to solve problem of relative imports --- website/docusaurus.config.js | 1 + 1 file changed, 1 insertion(+) diff --git a/website/docusaurus.config.js b/website/docusaurus.config.js index fa15f0a8f8..1e9b8a5194 100644 --- a/website/docusaurus.config.js +++ b/website/docusaurus.config.js @@ -9,6 +9,7 @@ module.exports = { onBrokenLinks: 'warn', onBrokenMarkdownLinks: 'warn', favicon: 'img/favicon.ico', + trailingSlash: false, organizationName: 'broadinstitute', // Usually your GitHub org/user name. projectName: 'warp', // Usually your repo name. plugins: [