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Arendt Group
Jbrowse2 Annelids
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!6
Nextflow work
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Merged
Nextflow work
nextflow_work
into
main
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6
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4
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Cyril Christophe Daniel Robert Cros
requested to merge
nextflow_work
into
main
10 months ago
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4484e589
Remove the testing branch always
· 4484e589
cyril.cros
authored
10 months ago
resources_to_s3_NF/jbrowse_script_slug.sh
+
18
−
5
Options
#!/bin/bash
## Gameplan is to parse the genomes and csv files
tail
-n
+1 tracks.csv |
sort
-t
,
-k
1,2 |
awk
-F
,
'$4=="VCF" { print "jbrowse add-track https://s3.embl.de/annelids/"$1"/variation/"$3".vcf.gz -a \""$1"\" -d \""$6"\" -n \""$3"\" --category \""$5"\""}'
>>
../image/jbrowse_script.sh
# Using this to filter above $4=="VCF"
\ No newline at end of file
#
# I am going to assume the CSV files have been patched with the s3 basename path - field 7 for tracks
#
# Genomes
tail
-n
+1 genomes.csv |
# it should not be genomes
sort
-t
,
-k1
,1 |
awk
-F
,
'{ print "jbrowse add-assembly https://s3.embl.de/annelids/"$1"/"$2" \
-n \""$1"\" --displayName \""$3"\"" }'
tail
-n
+1 tracks.csv |
# it should not be tracks
sort
-t
,
-k1
,1
-k5
,5
-k2
,2 |
awk
-F
,
'{ print "jbrowse add-track https://s3.embl.de/annelids/"$1"/"$5"/"$3".vcf.gz \
-a \""$1"\" -d \""$6"\" -n \""$3"\" --category \""$5"\""}'
# Text-indices
tail
-n
+1 tracks.csv |
awk
'$1 {print;}'
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