nftignore cleanup

Author: dialvarezs

tests/.nftignore

@@ -1,23 +1,30 @@
 .DS_Store
-Annotation/Prokka/**/*.{log,gbk,sqn}
-Assembly/**/QC/**/*.{html,log,pdf}
-Assembly/**/QUAST/**/*.{pdf,log,html,pdf}
+Annotation/Prokka/**/*.{log,err,gbk,sqn}
+Annotation/Prokka/**/*.tmp.*
+Assembly/*/QC/*/QUAST/*.{pdf,html,log}
+Assembly/*/QC/*/QUAST/**/*.{pdf,html}
 Assembly/MEGAHIT/*.log
 Assembly/MEGAHIT/QC/*/*.bowtie2.log
 Assembly/SPAdes/*.log
-GenomeBinning/*.tsv
+GenomeBinning/CONCOCT/stats/*_{original,PCA_components,PCA_transformed}_data_gt1000.csv
+GenomeBinning/CONCOCT/stats/*_log.txt
+GenomeBinning/CONCOCT/stats/*.tsv
+GenomeBinning/DASTool/*.log
 GenomeBinning/depths/**/*-depth.txt.gz
 GenomeBinning/depths/bins/*.png
 GenomeBinning/depths/bins/*.tsv
 GenomeBinning/MetaBAT2/unbinned/discarded/*.unbinned.pooled.fa.gz
-GenomeBinning/QC/*.tsv
-GenomeBinning/QC/BUSCO/**/*.{fa,json,txt,log,checkpoint,faa,fna,tsv}
-GenomeBinning/QC/BUSCO/**/busco_sequences/**
-GenomeBinning/QC/BUSCO/**/logs/**
-GenomeBinning/QC/CheckM2/**/DIAMOND_RESULTS.tsv
-GenomeBinning/QC/CheckM2/*/checkm2.log
-GenomeBinning/QC/QUAST/*.tsv
-GenomeBinning/QC/QUAST/**/*.{pdf,log,html,tsv}
+GenomeBinning/QC/busco_summary.tsv
+GenomeBinning/QC/BUSCO/**/.checkpoint
+GenomeBinning/QC/BUSCO/**/{logs,prodigal_output,busco_sequences}/**
+GenomeBinning/QC/BUSCO/**/*.json
+GenomeBinning/QC/BUSCO/**/*.log
+GenomeBinning/QC/BUSCO/**/*.txt
+GenomeBinning/QC/BUSCO/**/short_summary*.{txt,json}
+GenomeBinning/QC/BUSCO/*/*{-busco.log,-busco.batch_summary.txt}
+GenomeBinning/QC/QUAST/*/*.{pdf,html,log}
+GenomeBinning/QC/QUAST/*/**/*.{pdf,html}
+GenomeBinning/SemiBin2/log/*.log
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
 multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_data/multiqc_data.json
@@ -31,8 +38,6 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 QC_shortreads/fastp/**/*.{html,json}
-QC_shortreads/fastqc/*.{html,zip}
+QC_shortreads/fastqc/*_fastqc.{html,zip}
 QC_shortreads/remove_phix/*.log
-Taxonomy/CAT/*.tsv
 Taxonomy/CAT/**/bins/*.log
-Taxonomy/GTDB-Tk/*.tsv