From eefdd6754fee09aba032ebaffadcfa3d21cf6713 Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Tue, 9 Jan 2024 22:41:58 +0000
Subject: [PATCH] Watchdog update, workshop progress, blacklisting fix, http
 remote provider change, more assertions, list_commands coloring fix

---
 workflow/rules/external_data.smk | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/workflow/rules/external_data.smk b/workflow/rules/external_data.smk
index 656808aa..03479d37 100644
--- a/workflow/rules/external_data.smk
+++ b/workflow/rules/external_data.smk
@@ -1,27 +1,16 @@
 import os
-
 # from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
 
 # HTTP = HTTPRemoteProvider()
 
+storage:
+    provider="http",
 
-rule dl_example_data:
-    input:
-        storage(
-            "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(
+        storage.http(
             "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/hg19.p13.plusMT.no_alt_analysis_set.fa.gz",
             keep_local=True,
         ),
@@ -42,7 +31,7 @@ rule download_hg19_reference:
 
 rule download_hg38_reference:
     input:
-        storage(
+        storage.http(
             "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.fa.gz",
             keep_local=True,
         ),
@@ -63,7 +52,7 @@ rule download_hg38_reference:
 
 rule download_T2T_reference:
     input:
-        storage(
+        storage.http(
             "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz",
             keep_local=True,
         ),
@@ -84,7 +73,7 @@ rule download_T2T_reference:
 
 rule download_mm10_reference:
     input:
-        storage(
+        storage.http(
             "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz",
             keep_local=True,
         ),
@@ -105,7 +94,7 @@ rule download_mm10_reference:
 
 rule download_T2T_tarball:
     input:
-        storage(
+        storage.http(
             "https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz",
             keep_local=True,
         ),
@@ -125,7 +114,7 @@ rule download_T2T_tarball:
 
 rule download_arbigent_mappability_track:
     input:
-        storage(
+        storage.http(
             "https://zenodo.org/record/7697400/files/mapping_counts_allchrs_hg38.txt",
             keep_local=True,
         ),
@@ -144,7 +133,7 @@ rule download_arbigent_mappability_track:
 rule download_scnova_data:
     input:
         ancient(
-            storage(
+            storage.http(
                 "https://zenodo.org/record/7697400/files/scNOVA_data_models.zip",
                 keep_local=True,
             )