diff --git a/bu_isciii/templates/genomeev/RESULTS/lablog b/bu_isciii/templates/genomeev/RESULTS/lablog index caa1f16f..c593c7ac 100644 --- a/bu_isciii/templates/genomeev/RESULTS/lablog +++ b/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 -