From 25092919206bef9737507b3d6a453437010d120d Mon Sep 17 00:00:00 2001 From: Maria Doyle Date: Wed, 18 Oct 2023 09:56:55 +0100 Subject: [PATCH] Fix zenodo links --- .../tutorials/crispr-screen/data-library.yaml | 20 +++++++++---------- .../tutorials/crispr-screen/tutorial.md | 20 +++++++++---------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/topics/genome-annotation/tutorials/crispr-screen/data-library.yaml b/topics/genome-annotation/tutorials/crispr-screen/data-library.yaml index bd605fae98d306..22d3d3dc414b9a 100644 --- a/topics/genome-annotation/tutorials/crispr-screen/data-library.yaml +++ b/topics/genome-annotation/tutorials/crispr-screen/data-library.yaml @@ -13,43 +13,43 @@ items: - name: 'DOI: 10.5281/zenodo.5750854' description: latest items: - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/adapters_list.tsv + - url: https://zenodo.org/records/5750854/files/adapter_list.tsv src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/brunello.tsv + - url: https://zenodo.org/records/5750854/files/brunello.tsv src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/h.all.v7.4.symbols.gmt + - url: https://zenodo.org/records/5750854/files/h.all.v7.4.symbols.gmt src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_count_summary.tsv + - url: https://zenodo.org/records/5750854/files/kenji_mageck_count_summary.tsv src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_count_report.pdf + - url: https://zenodo.org/records/5750854/files/kenji_mageck_count_report.pdf src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_sgrna_counts.tsv + - url: https://zenodo.org/records/5750854/files/kenji_mageck_sgrna_counts.tsv src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_mle_design_matrix.tsv + - url: https://zenodo.org/records/5750854/files/kenji_mageck_mle_design_matrix.tsv src: url ext: tsv info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T0-Control.fastq.gz + - url: https://zenodo.org/records/5750854/files/T0-Control.fastq.gz src: url ext: gz info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T8-APR-246.fastq.gz + - url: https://zenodo.org/records/5750854/files/T8-APR-246.fastq.gz src: url ext: gz info: https://zenodo.org/record/5750854 - - url: https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T8-Vehicle.fastq.gz + - url: https://zenodo.org/records/5750854/files/T8-Vehicle.fastq.gz src: url ext: gz info: https://zenodo.org/record/5750854 diff --git a/topics/genome-annotation/tutorials/crispr-screen/tutorial.md b/topics/genome-annotation/tutorials/crispr-screen/tutorial.md index 021f3c46473968..fa026603b3e6d7 100644 --- a/topics/genome-annotation/tutorials/crispr-screen/tutorial.md +++ b/topics/genome-annotation/tutorials/crispr-screen/tutorial.md @@ -78,9 +78,9 @@ Here we will demonstrate analysing {CRISPR} screen using data from {% cite Fujih > - Copy the following tabular data, paste it into the textbox and press Build > > ``` -> T0-Control https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T0-Control.fastq.gz -> T8-APR-246 https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T8-APR-246.fastq.gz -> T8-Vehicle https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/T8-Vehicle.fastq.gz +> T0-Control https://zenodo.org/records/5750854/files/T0-Control.fastq.gz +> T8-APR-246 https://zenodo.org/records/5750854/files/T8-APR-246.fastq.gz +> T8-Vehicle https://zenodo.org/records/5750854/files/T8-Vehicle.fastq.gz > ``` > > ![Rule-based Uploader](../../images/crispr-screen/crispr_rule_uploader.png) @@ -118,7 +118,7 @@ With CRISPR screens we expect adapter sequence to be present, surrounding the gu > > 1. Import the adapters file from [Zenodo]({{ page.zenodo_link }}) or the Shared Data library (if available): > ``` -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/adapter_list.tsv +> https://zenodo.org/records/5750854/files/adapter_list.tsv > ``` > {% snippet faqs/galaxy/datasets_import_via_link.md %} > @@ -246,7 +246,7 @@ To count how many guides we have for each gene, we need a library file that tell > Count guides per gene > 1. Import the sgRNA library file > ``` -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/brunello.tsv +> https://zenodo.org/records/5750854/files/brunello.tsv > ``` > > 2. {% tool [MAGeCK count](toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4) %} with the following parameters: @@ -259,9 +259,9 @@ To count how many guides we have for each gene, we need a library file that tell > > 3. We have been using 1% of reads from the samples. Import the MAGeCK count files (sgRNA counts, counts summary and plots pdf) for the full dataset so you can see what results for a real dataset looks like. > ``` -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_sgrna_counts.tsv -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_count_summary.tsv -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_count_report.pdf +> https://zenodo.org/records/5750854/files/kenji_mageck_sgrna_counts.tsv +> https://zenodo.org/records/5750854/files/kenji_mageck_count_summary.tsv +> https://zenodo.org/records/5750854/files/kenji_mageck_count_report.pdf > ``` > {: .hands_on} @@ -569,7 +569,7 @@ We can perform pathway analysis on the results to identify pathways that are cha > > 1. Import the Hallmark pathways file [Zenodo]({{ page.zenodo_link }}) or the Shared Data library (if available). Set the Type to tabular: > ``` -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/h.all.v7.4.symbols.gmt +> https://zenodo.org/records/5750854/files/h.all.v7.4.symbols.gmt > ``` > {% snippet faqs/galaxy/datasets_change_datatype.md %} > @@ -629,7 +629,7 @@ Examples of more complicated design matrices, for e.g. time series experiments, > Test for enrichment with MLE > 1. Import the design matrix file from [Zenodo]({{ page.zenodo_link }}) or the Shared Data library (if available): > ``` -> https://zenodo.org/api/files/6599878c-f569-41bf-a37a-2c6f3d2e67f9/kenji_mageck_mle_design_matrix.tsv +> https://zenodo.org/records/5750854/files/kenji_mageck_mle_design_matrix.tsv > ``` > > 2. {% tool [MAGeCKs mle](toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.9.2.1) %} with the following parameters: