adapts ensembl URLs according to recent changes [ci skip]

modules/data_download/Snakefile

@@ -30,7 +30,7 @@ def get_gtf_file(wildcards):
 rule get_gtf_file:
      output: "data/{genus_species}.{build}.{ensembl_release}.chr.gtf"
      params: get_species
-     shell: "rsync -av rsync://ftp.ensembl.org/ensembl/pub/release-{config[ensembl_release]}/gtf/{params}/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf.gz data/ && gunzip data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf.gz && sed 's/^chr//g' data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf > tmp && mv tmp data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf"
+     shell: "rsync -av rsync://ftp.ensembl.org/pub/release-{config[ensembl_release]}/gtf/{params}/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf.gz data/ && gunzip data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf.gz && sed 's/^chr//g' data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf > tmp && mv tmp data/{wildcards.genus_species}.{wildcards.build}.{config[ensembl_release]}.chr.gtf"
 
 rule modify_gtf_file: # remove 'chr' prefix if it exists in the gtf file - remove contigs and mitochondrial records
         input: "data/{species_prefix}.{ensembl_release}.chr.gtf"
@@ -48,18 +48,18 @@ rule get_transcript_ids:
 rule download_toplevel_dna:
 	output: "data/{genus_species}.{build}.dna.toplevel.fa.gz"
 	params: get_species
-	shell: "rsync -av rsync://ftp.ensembl.org/ensembl/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.toplevel.fa.gz data/"
+	shell: "rsync -av rsync://ftp.ensembl.org/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.toplevel.fa.gz data/"
 
 rule download_primary_assembly_dna:
         output: "data/{genus_species}.{build}.dna.primary_assembly.fa.gz"
         params: get_species
-        shell: "rsync -av rsync://ftp.ensembl.org/ensembl/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.primary_assembly.fa.gz data/"
+        shell: "rsync -av rsync://ftp.ensembl.org/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.primary_assembly.fa.gz data/"
 
 rule download_chromsomal_dna:
         input:
         output: "data/{genus_species}.{build}.dna.chromosome.{chrom}.fa.gz"
         params: get_species
-        shell: "rsync -av rsync://ftp.ensembl.org/ensembl/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.chromosome.{wildcards.chrom}.fa.gz data/"
+        shell: "rsync -av rsync://ftp.ensembl.org/pub/release-{config[ensembl_release]}/fasta/{params}/dna/{wildcards.genus_species}.{wildcards.build}.dna.chromosome.{wildcards.chrom}.fa.gz data/"
 
 rule decompress_dna_file:
         input: "data/{species_prefix}.dna.{assembly_level}.fa.gz"
@@ -85,7 +85,7 @@ rule download_maf_files_mouse:
 rule download_cdna_file:
         output: "data/{genus_species}.{build}.cdna.all.fa.gz"
         params: get_species
-        shell: "rsync -av rsync://ftp.ensembl.org/ensembl/pub/release-{config[ensembl_release]}/fasta/{params}/cdna/{wildcards.genus_species}.{wildcards.build}.cdna.all.fa.gz data"
+        shell: "rsync -av rsync://ftp.ensembl.org/pub/release-{config[ensembl_release]}/fasta/{params}/cdna/{wildcards.genus_species}.{wildcards.build}.cdna.all.fa.gz data"
 
 rule decompress_cdna_file:
         input: "data/{species_prefix}.cdna.all.fa.gz"