Avoid using wget timestamping (-N) with -O option

timestamping does not work with -O, and avoiding having these together
avoids confusing error messages during failures

Author: chapmanb

ggd-recipes/GRCh37/cosmic.yaml

@@ -10,8 +10,8 @@ recipe:
         baseurl=https://s3.amazonaws.com/biodata/variants/cosmic-v68-GRCh37.vcf.gz
         mkdir -p variation
         cd variation
-        wget --no-check-certificate -c -O cosmic.vcf.gz -N $baseurl
-        wget --no-check-certificate -c -O cosmic.vcf.gz.tbi -N $baseurl.tbi
+        wget --no-check-certificate -c -O cosmic.vcf.gz $baseurl
+        wget --no-check-certificate -c -O cosmic.vcf.gz.tbi $baseurl.tbi
     recipe_outfiles:
         - variation/cosmic.vcf.gz
         - variation/cosmic.vcf.gz.tbi

ggd-recipes/TAIR10/mirbase.yaml

@@ -11,15 +11,15 @@ recipe:
         mkdir -p srnaseq
         cd srnaseq
 
-        wget -N -c -O tmp.gtf.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.gff.gz
+        wget -c -O tmp.gtf.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.gff.gz
         zgrep -v exon tmp.gtf.gz | grep -v region | sed 's/Name/name/g' | sed 's/=/ /g' > srna-transcripts.gtf
-        wget -N -c -O hairpin.t.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz && gunzip -f hairpin.t.fa.gz
+        wget -c -O hairpin.t.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz && gunzip -f hairpin.t.fa.gz
         cat hairpin.t.fa | awk '{if ($0~/>ath/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > hairpin.fa
-        wget -N -c -O mature.t.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz && gunzip -f mature.t.fa.gz
+        wget -c -O mature.t.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz && gunzip -f mature.t.fa.gz
         cat mature.t.fa | awk '{if ($0~/>ath/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
-        wget -N -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz && gunzip -f miRNA.t.str.gz
+        wget -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz && gunzip -f miRNA.t.str.gz
         cat miRNA.t.str | awk '{if ($0~/ath/)print $0}' > miRNA.str
-        wget --no-check-certificate -N -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip -f Rfam_for_miRDeep.fa.gz
+        wget --no-check-certificate -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip -f Rfam_for_miRDeep.fa.gz
     recipe_outfiles:
         - srnaseq/srna-transcripts.gtf
         - srnaseq/hairpin.fa

ggd-recipes/canFam3/mirbase.yaml

@@ -10,23 +10,23 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -q -N -c -O cfa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
+        wget --random-wait --retry-connrefused -q -c -O cfa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
         awk '$3=="miRNA"' cfa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -q -N -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/rmsk.txt.gz
+        wget  --random-wait --retry-connrefused -q -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/rmsk.txt.gz
         zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused  -q -N -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/refGene.txt.gz
+        wget  --random-wait --retry-connrefused  -q -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/refGene.txt.gz
         zcat refGene.txt.gz | awk '{print $3"\t.\tgene\t"$5"\t"$6"\t.\t"$4"\t.\tname "$13";"}' >> srna-transcripts.gtf
         # mirbase
-        wget  --random-wait --retry-connrefused  -q -N -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
+        wget  --random-wait --retry-connrefused  -q -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
         zcat hairpin.fa.gz |  awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > hairpin.fa
-        wget  --random-wait --retry-connrefused  -q -N -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
+        wget  --random-wait --retry-connrefused  -q -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
         zcat mature.fa.gz |  awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
-        wget  --random-wait --retry-connrefused  -q -N -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
+        wget  --random-wait --retry-connrefused  -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/cfa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -q -N -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
+        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
         # mintmap
         # mirdeep2
-        wget  --random-wait --retry-connrefused --no-check-certificate -q -N -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
+        wget  --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
         # targetscan analysis
     recipe_outfiles:
         - srnaseq/srna-transcripts.gtf

ggd-recipes/hg19/cosmic.yaml

@@ -10,8 +10,8 @@ recipe:
         baseurl=https://s3.amazonaws.com/biodata/variants/cosmic-v68-hg19.vcf.gz
         mkdir -p variation
         cd variation
-        wget --no-check-certificate -c -O cosmic.vcf.gz -N $baseurl
-        wget --no-check-certificate -c -O cosmic.vcf.gz.tbi -N $baseurl.tbi
+        wget --no-check-certificate -c -O cosmic.vcf.gz $baseurl
+        wget --no-check-certificate -c -O cosmic.vcf.gz.tbi $baseurl.tbi
     recipe_outfiles:
         - variation/cosmic.vcf.gz
         - variation/cosmic.vcf.gz.tbi

ggd-recipes/hg19/mirbase.yaml

@@ -10,37 +10,37 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -nv -N -c -O hsahg19.gff3 ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -nv -c -O hsahg19.gff3 ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3
         awk '$3=="miRNA"' hsahg19.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -nv -N -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
+        wget  --random-wait --retry-connrefused -nv -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
         zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -nv -N -c -O tRNAs.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/tRNAs.txt.gz
+        wget  --random-wait --retry-connrefused -nv -c -O tRNAs.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/tRNAs.txt.gz
         zcat tRNAs.txt.gz | awk '{print $2"\t.\ttRNA\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -nv -N -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
+        wget  --random-wait --retry-connrefused -nv -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
         zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused  -nv -N -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
+        wget  --random-wait --retry-connrefused  -nv -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
         zcat refGene.txt.gz | awk '{print $3"\t.\tgene\t"$5"\t"$6"\t.\t"$4"\t.\tname "$13";"}' >> srna-transcripts.gtf
-        # wget --random-wait --retry-connrefused  -nv -N -c -O piR_hg19_v1.0.bed.gz http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
+        # wget --random-wait --retry-connrefused  -nv -c -O piR_hg19_v1.0.bed.gz http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
         # zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf
         # mirbase
-        wget  --random-wait --retry-connrefused  -nv -N -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
+        wget  --random-wait --retry-connrefused  -nv -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
         zcat hairpin.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > hairpin.fa
-        wget  --random-wait --retry-connrefused  -nv -N -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
+        wget  --random-wait --retry-connrefused  -nv -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
         zcat mature.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
-        wget  --random-wait --retry-connrefused  -nv -N -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
+        wget  --random-wait --retry-connrefused  -nv -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -nv -N -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
         # tdrmapper
-        wget   --random-wait --retry-connrefused  --no-check-certificate -nv -N -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
+        wget   --random-wait --retry-connrefused  --no-check-certificate -nv -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
         # mintmap
         wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/LookupTable.tRFs.MINTmap_v1.txt
         wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/tRNAspace.Spliced.Sequences.MINTmap_v1.fa
         wget  --random-wait --retry-connrefused  --no-check-certificate -nv -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/OtherAnnotations.MINTmap_v1.txt
         # mirdeep2
-        wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
+        wget  --random-wait --retry-connrefused --no-check-certificate -nv -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
         # targetscan analysis
-        wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c -O Summary_Counts.txt.zip http://www.targetscan.org/vert_71/vert_71_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip
-        wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c -O miR_Family_Info.txt.zip http://www.targetscan.org/vert_71/vert_71_data_download/miR_Family_Info.txt.zip && unzip miR_Family_Info.txt.zip
+        wget  --random-wait --retry-connrefused --no-check-certificate -nv -c -O Summary_Counts.txt.zip http://www.targetscan.org/vert_71/vert_71_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip
+        wget  --random-wait --retry-connrefused --no-check-certificate -nv -c -O miR_Family_Info.txt.zip http://www.targetscan.org/vert_71/vert_71_data_download/miR_Family_Info.txt.zip && unzip miR_Family_Info.txt.zip
         wget  --random-wait --retry-connrefused --no-check-certificate -nv -N -c ftp://mirbase.org/pub/mirbase/21/database_files/mirna_mature.txt.gz
     recipe_outfiles:
         - srnaseq/srna-transcripts.gtf

ggd-recipes/hg19/rmsk.yaml

@@ -10,7 +10,7 @@ recipe:
       - |
         mkdir -p coverage/problem_regions/repeats
         cd coverage/problem_regions/repeats
-        wget  --random-wait --retry-connrefused -q -N -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
+        wget  --random-wait --retry-connrefused -q -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
         zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' | gzip > rmsk.gtf.gz
     recipe_outfiles:
       - coverage/problem_regions/repeats/rmsk.gtf.gz

ggd-recipes/hg38-noalt/mirbase.yaml

@@ -10,35 +10,35 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -q -N -c -O hsa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
         awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -q -N -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz
+        wget  --random-wait --retry-connrefused -q -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz
         zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -q -N -c -O tRNAs.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/tRNAs.txt.gz
+        wget  --random-wait --retry-connrefused -q -c -O tRNAs.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/tRNAs.txt.gz
         zcat tRNAs.txt.gz | awk '{print $2"\t.\ttRNA\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused -q -N -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz
+        wget  --random-wait --retry-connrefused -q -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz
         zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf
-        wget  --random-wait --retry-connrefused  -q -N -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
+        wget  --random-wait --retry-connrefused  -q -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
         zcat refGene.txt.gz | awk '{print $3"\t.\tgene\t"$5"\t"$6"\t.\t"$4"\t.\tname "$13";"}' >> srna-transcripts.gtf
         sed -i 's/\t0\t/\t1\t/' srna-transcripts.gtf
         # wget http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
         # zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf
         # mirbase
-        wget  --random-wait --retry-connrefused  -q -N -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
+        wget  --random-wait --retry-connrefused  -q -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
         zcat hairpin.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > hairpin.fa
-        wget  --random-wait --retry-connrefused  -q -N -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
+        wget  --random-wait --retry-connrefused  -q -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
         zcat mature.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
-        wget  --random-wait --retry-connrefused  -q -N -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
+        wget  --random-wait --retry-connrefused  -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -q -N -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/hsa.gff3
         #tdrmapper
-        wget   --random-wait --retry-connrefused  --no-check-certificate -q -N -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
+        wget   --random-wait --retry-connrefused  --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
         # mintmap
         wget  --random-wait --retry-connrefused --no-check-certificate -q -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/LookupTable.tRFs.MINTmap_v1.txt
         wget  --random-wait --retry-connrefused --no-check-certificate -q -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/tRNAspace.Spliced.Sequences.MINTmap_v1.fa
         wget  --random-wait --retry-connrefused  --no-check-certificate -q -N -c https://github.com/TJU-CMC-Org/MINTmap/raw/master/OtherAnnotations.MINTmap_v1.txt
         # mirdeep2
-        wget  --random-wait --retry-connrefused --no-check-certificate -q -N -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
+        wget  --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
         # targetscan analysis
     recipe_outfiles:
         - srnaseq/srna-transcripts.gtf