Redesigned support for URL to host genome

cbg-ethz · Mar 12, 2022 · d77fa11 · d77fa11
1 parent 0dd9c72
commit d77fa11
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 4 deletions.
diff --git a/workflow/rules/dehuman.smk b/workflow/rules/dehuman.smk
@@ -1,6 +1,10 @@
 from functools import partial
 
 
+localrules:
+    download_host_ref,
+
+
 rule dh_reuse_alignreject:
     # "rely on aligner's output".
     # this rule re-use the rejected reads in align.smk (e.g. ngshmmalign's /alignments/rejects.sam)
@@ -83,10 +87,21 @@ rule dh_redo_alignreject:
         """
 
 
+rule download_host_ref:
+    output:
+        host_ref=config.dehuman["ref_host"],
+    params:
+        host_ref_url=config.dehuman["ref_host_url"],
+    shell:
+        """
+        curl --output "{output.host_ref}" "{params.host_ref_url}"
+        """
+
+
 rule dh_hostalign:
     input:
-        host_ref=cachepath(config.dehuman["ref_host"]),
-        ref_index=multiext(cachepath(config.dehuman["ref_host"]), *bwa_idx_ext),
+        host_ref=config.dehuman["ref_host"],
+        ref_index=multiext(config.dehuman["ref_host"], *bwa_idx_ext),
         reject_1=rules.dh_redo_alignreject.output.reject_1
         if config["dehuman"]["catchup"]
         else rules.dh_reuse_alignreject.output.reject_1,

diff --git a/workflow/schemas/config_schema.json b/workflow/schemas/config_schema.json
@@ -1267,10 +1267,16 @@
                     "default": 4
                 },
                 "ref_host": {
+                    "type": "string",
+                    "default": "references/human.fa.gz",
+                    "description": "Host's genome used to remove reads (e.g. human genome)\n\n**Note:** if this file is absent, it is possible to fetch it from a remote server, see property `ref_host_url` below.",
+                    "examples": ["/cluster/project/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa"]
+                },
+                "ref_host_url": {
                     "type": "string",
                     "default": "http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
-                    "description": "Host's genome used to remove reads (e.g. human genome)\n\n**Note:** although directly fetching the reference from the network can work, we _strongly advise_ to use local files (e.g., download the reference locally or use one provided by your cluster).",
-                    "examples": ["references/human.fa", "/cluster/project/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa", "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz"]
+                    "description": "If the host's genome specified in property `ref_host` isn't present, fetch it from a remote server.\n\n**Note** remember to set aside enough memory for the indexing rule, see section `ref_bwa_index` property `mem`.",
+                    "examples": [ "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz"]
                 },
                 "keep_host": {
                     "type": "boolean",