Introduced handling of Influenza-C in IRMA template and small fixes in viralrecon and exometrio #177
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…be used for single files
svarona
reviewed
Jan 15, 2024
| cd blast; ln -s ../../../ANALYSIS/*/*.blast.filt.header.xlsx .; cd - |
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En vez de hacer un link a todos los BLAST, sería mejor hacer el link del BLAST con todo solo no?
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Changed *.blast.filt.header.xlsx for all_samples_filtered_BLAST_results.xlsx
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@Shettland acuérdate de que pase el lintin! |
svarona
reviewed
Jan 16, 2024
| @@ -46,4 +46,4 @@ cd mapping_consensus; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; d | |||
| cd variants_annot; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/variants/ivar/snpeff/${arr[0]}.snpsift.txt ./${arr[0]}_${arr[1]}.snpsift.txt; done; cd - | |||
| cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd - | |||
| cd abacas_assembly; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/assembly/spades/rnaviral/abacas/${arr[0]}.abacas.fasta ./${arr[0]}_${arr[1]}.abacas.fasta; done; cd - | |||
| cd blast; ln -s ../../../ANALYSIS/*/*.blast.filt.header.xlsx .; cd - | |||
| cd blast; ln -s ../../../ANALYSIS/*/all_samples_filtered_BLAST_results.xlsx . ; cd - | |||
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Maybe for just one excel there is no need to create a blast folder, maybe you can put it on the main results folder?
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Several changes were introduced for irma's
lablogandcreate_irma_stats.shin order to extract data from Influenza-C samples when present in service. Also some fixes and implementations inviralrecon_resultsandexcel_generator.pyPASS_ONLYline was commented in exometrio'sexomiser_configfile.ymland a deprecated line removingspring.logwas deleted from03-annotation/lablogin this template