Nextflow work

Merging to initiate a dev/prod/setup

resources_to_s3_NF/jbrowse_script_slug.sh

 #!/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;}'