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friendsofstrandseq · Jan 9, 2024 · 82d629f · 82d629f
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -48,11 +48,11 @@ jobs:
         with:
           directory: .
           snakefile: ./workflow/Snakefile
-          # stagein: "conda config --set channel_priority flexible && mamba install -c bioconda snakemake-storage-plugin-http"
-          args: "--cores 1 --software-deployment-method conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
       - name: Testing report
         uses: snakemake/snakemake-github-action@v1.24.0
         with:
           directory: .
           snakefile: ./workflow/Snakefile
-          args: "--cores 1 --software-deployment-method conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --report report.zip"
+          args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml  --conda-frontend mamba --report report.zip"
diff --git a/README.md b/README.md
@@ -102,12 +102,12 @@ the workflow goes through the following steps:
 
 # 📕 References
 
+> MosaiCatcher v2 publication: Weber Thomas, Marco Raffaele Cosenza, and Jan Korbel. 2023. ‘MosaiCatcher v2: A Single-Cell Structural Variations Detection and Analysis Reference Framework Based on Strand-Seq’. Bioinformatics 39 (11): btad633. https://doi.org/10.1093/bioinformatics/btad633.
+
 > Strand-seq publication: Falconer, E., Hills, M., Naumann, U. et al. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9, 1107–1112 (2012). https://doi.org/10.1038/nmeth.2206
 
 > scTRIP/MosaiCatcher original publication: Sanders, A.D., Meiers, S., Ghareghani, M. et al. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol 38, 343–354 (2020). https://doi.org/10.1038/s41587-019-0366-x
 
 > ArbiGent publication: Porubsky, David, Wolfram Höps, Hufsah Ashraf, PingHsun Hsieh, Bernardo Rodriguez-Martin, Feyza Yilmaz, Jana Ebler, et al. 2022. “Recurrent Inversion Polymorphisms in Humans Associate with Genetic Instability and Genomic Disorders.” Cell 185 (11): 1986-2005.e26. https://doi.org/10.1016/j.cell.2022.04.017.
 
 > scNOVA publication: Jeong, Hyobin, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, et al. 2022. “Functional Analysis of Structural Variants in Single Cells Using Strand-Seq.” Nature Biotechnology, November, 1–13. https://doi.org/10.1038/s41587-022-01551-4.
-
-> scNOVA publication: Jeong, Hyobin, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, et al. 2022. “Functional Analysis of Structural Variants in Single Cells Using Strand-Seq.” Nature Biotechnology, November, 1–13. https://doi.org/10.1038/s41587-022-01551-4.
diff --git a/workflow/rules/external_data.smk b/workflow/rules/external_data.smk
@@ -1,16 +1,26 @@
 import os
-# from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
+from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
 
-# HTTP = HTTPRemoteProvider()
+HTTP = HTTPRemoteProvider()
 
-storage:
-    provider="http",
 
+rule dl_example_data:
+    input:
+        HTTP.remote(
+            "https://sandbox.zenodo.org/record/1074721/files/TEST_EXAMPLE_DATA.zip",
+            keep_local=True,
+        ),
+    output:
+        touch("config/dl_example_data.ok"),
+    log:
+        touch("log/config/dl_example_data.ok"),
+    run:
+        shell("unzip {input} -d .")
 
 
 rule download_hg19_reference:
     input:
-        storage.http(
+        HTTP.remote(
             "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/hg19.p13.plusMT.no_alt_analysis_set.fa.gz",
             keep_local=True,
         ),
@@ -31,7 +41,7 @@ rule download_hg19_reference:
 
 rule download_hg38_reference:
     input:
-        storage.http(
+        HTTP.remote(
             "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.fa.gz",
             keep_local=True,
         ),
@@ -52,7 +62,7 @@ rule download_hg38_reference:
 
 rule download_T2T_reference:
     input:
-        storage.http(
+        HTTP.remote(
             "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz",
             keep_local=True,
         ),
@@ -73,7 +83,7 @@ rule download_T2T_reference:
 
 rule download_mm10_reference:
     input:
-        storage.http(
+        HTTP.remote(
             "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz",
             keep_local=True,
         ),
@@ -94,7 +104,7 @@ rule download_mm10_reference:
 
 rule download_T2T_tarball:
     input:
-        storage.http(
+        HTTP.remote(
             "https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz",
             keep_local=True,
         ),
@@ -114,7 +124,7 @@ rule download_T2T_tarball:
 
 rule download_arbigent_mappability_track:
     input:
-        storage.http(
+        HTTP.remote(
             "https://zenodo.org/record/7697400/files/mapping_counts_allchrs_hg38.txt",
             keep_local=True,
         ),
@@ -133,7 +143,7 @@ rule download_arbigent_mappability_track:
 rule download_scnova_data:
     input:
         ancient(
-            storage.http(
+            HTTP.remote(
                 "https://zenodo.org/record/7697400/files/scNOVA_data_models.zip",
                 keep_local=True,
             )