results lablog working!

bu_isciii/templates/genomeev/RESULTS/lablog

@@ -1,16 +1,17 @@
+# conda activate 2excel
 mkdir $(date '+%Y%m%d')_entrega01
 cd $(date '+%Y%m%d')_entrega01
 
-# Create directories depending on the analysis
+#Create directories depending on the analysis
 mkdir assembly_spades
 mkdir blast
 
-# Create symbolic links depending on the analysis
-# Individual files
+#Create symbolic links depending on the analysis
+#Individual files
 ln -s ../../ANALYSIS/*_MAG/99-stats/multiqc_report.html ./krona_results.html
 ln -s ../../ANALYSIS/*/assembly_stats.xlsx ./assembly_stats.xlsx
-ln -s ../../ANALYSIS/*/01-PikaVirus-results/all_samples_virus_table_filtered.xlsx ./filtered_all_samples_virus_table.xlsx
+python /scratch/bi/pipelines/utilities/export_excel_from_csv.py --input_file ../../ANALYSIS/*PIKAVIRUS*/*/all_samples_virus_table_filtered.tsv --delimiter '\t' --output_filename filtered_all_samples_virus_table --it_has_index --it_has_header
 
-# Folders
-cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd -
-cd blast; ln -s ../../../ANALYSIS/*/*.blast.filt.header.xlsx .; cd -
+#Folders
+cd assembly_spades; ln -s ../../../ANALYSIS/*BLAST*/*/*scaffolds.fa .; cd -
+cd blast; ln -s ../../../ANALYSIS/*BLAST*/all_samples_filtered_BLAST_results.xlsx .; ln -s ../../../ANALYSIS/*BLAST*/*/*.xlsx .; cd -