mkdir $(date '+%Y%m%d')_entrega01
cd $(date '+%Y%m%d')_entrega01

#Create directories depending on the analysis
mkdir mapping_consensus 
mkdir variants_annot
mkdir assembly_spades
mkdir abacas_assembly
mkdir blast

#Create symbolic links depending on the analysis
#Individual files
ln -s ../../ANALYSIS/*_MAG/99-stats/multiqc_report.html ./krona_results.html
ln -s ../../ANALYSIS/*/mapping_illumina*.xlsx ./mapping_illumina.xlsx
ln -s ../../ANALYSIS/*/*/variants/ivar/variants_long_table*.xlsx ./
ln -s ../../ANALYSIS/*/*/variants/ivar/consensus/bcftools/pangolin/pangolin.xlsx ./pangolin.xlsx
ln -s ../../ANALYSIS/*/*/variants/ivar/consensus/bcftools/nextclade/nextclade.xlsx ./nextclade.xlsx
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

#Folders
cd mapping_consensus;ln -s ../../../ANALYSIS/*/*/variants/ivar/consensus/bcftools/*.consensus.fa .; cd -
cd variants_annot; ln -s ../../../ANALYSIS/*/*/variants/ivar/snpeff/*.snpsift.txt .; cd -
cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd -
cd abacas_assembly; ln -s ../../../ANALYSIS/*/*/assembly/spades/rnaviral/abacas/*.abacas.fasta .; cd -
cd blast; ln -s ../../../ANALYSIS/*/*.blast.filt.header.xlsx .; cd -
