diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 57c11414..2aff4792 100644 --- 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 index 5119ff39..41514b10 100644 --- a/README.md +++ b/README.md @@ -102,6 +102,8 @@ 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 @@ -109,5 +111,3 @@ the workflow goes through the following steps: > 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 index 03479d37..634ac216 100644 --- 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, )