Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 37:14ae3bb73e02 draft

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Uploaded
author jackcurragh
date Fri, 23 Sep 2022 14:30:47 +0000
parents ecf172071e80
children 252a1899f3af
files get_chrom_sizes/get_chrom_sizes.xml
diffstat 1 files changed, 1 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:19:34 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:30:47 2022 +0000
@@ -3,8 +3,7 @@
     <command>
 
         #if $refGenomeSource.genomeSource == "builtin":
-            cat "#chrom\tlength" > $output1
-            cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat >> $output1
+            cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
         #else:
             cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
         #end if