update nftignore

Author: maxulysse

tests/.nftignore

@@ -1,27 +1,76 @@
 bbsplit/*.stats.txt
-fastqc/*/*fastqc.{html,zip}
+fastqc/*/*.{html,zip}
 kallisto/*/abundance.{h5,tsv}
 kallisto/*/kallisto_quant.log
 kallisto/*/run_info.json
 kallisto/kallisto.*
-multiqc/multiqc_report.html
-multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
-multiqc/multiqc_report_data/kallisto_alignment.txt
-multiqc/multiqc_report_data/multiqc.log
-multiqc/multiqc_report_data/multiqc_data.json
-multiqc/multiqc_report_data/multiqc_general_stats.txt
-multiqc/multiqc_report_data/multiqc_kallisto.txt
-multiqc/multiqc_report_data/multiqc_salmon.txt
-multiqc/multiqc_report_data/multiqc_software_versions.txt
-multiqc/multiqc_report_data/multiqc_sources.txt
-multiqc/multiqc_report_data/salmon_plot.txt
-multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
+multiqc/**/multiqc_report.html
+multiqc/**/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
+multiqc/**/multiqc_report_data/junction_saturation_known.txt
+multiqc/**/multiqc_report_data/junction_saturation_novel.txt
+multiqc/**/multiqc_report_data/kallisto_alignment.txt
+multiqc/**/multiqc_report_data/multiqc.log
+multiqc/**/multiqc_report_data/multiqc_data.json
+multiqc/**/multiqc_report_data/multiqc_dupradar.txt
+multiqc/**/multiqc_report_data/multiqc_fail_strand_check_table.txt
+multiqc/**/multiqc_report_data/multiqc_general_stats.txt
+multiqc/**/multiqc_report_data/multiqc_kallisto.txt
+multiqc/**/multiqc_report_data/multiqc_picard_dups.txt
+multiqc/**/multiqc_report_data/multiqc_rseqc_bam_stat.txt
+multiqc/**/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
+multiqc/**/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
+multiqc/**/multiqc_report_data/multiqc_rseqc_read_distribution.txt
+multiqc/**/multiqc_report_data/multiqc_salmon.txt
+multiqc/**/multiqc_report_data/multiqc_sample-relationships*.txt
+multiqc/**/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
+multiqc/**/multiqc_report_data/multiqc_software_versions.txt
+multiqc/**/multiqc_report_data/multiqc_sources.txt
+multiqc/**/multiqc_report_data/multiqc_star.txt
+multiqc/**/multiqc_report_data/picard_deduplication.txt
+multiqc/**/multiqc_report_data/qualimap_genomic_origin.txt
+multiqc/**/multiqc_report_data/qualimap_rnaseq_genome_results.txt
+multiqc/**/multiqc_report_data/rseqc_bam_stat.txt
+multiqc/**/multiqc_report_data/rseqc_inner_distance*.txt
+multiqc/**/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
+multiqc/**/multiqc_report_data/rseqc_read_*.txt
+multiqc/**/multiqc_report_data/salmon_plot.txt
+multiqc/**/multiqc_report_data/samtools-flagstat-dp_*.txt
+multiqc/**/multiqc_report_data/samtools-stats-dp.txt
+multiqc/**/multiqc_report_data/samtools_alignment_plot.txt
+multiqc/**/multiqc_report_data/star_alignment_plot.txt
+multiqc/**/multiqc_report_data/star_summary_table.txt
+multiqc/**/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
 pipeline_info/*.{html,json,txt,yml}
-salmon/*/aux_info/fld.gz
-salmon/*/aux_info/meta_info.json
-salmon/*/libParams/flenDist.txt
-salmon/*/logs/salmon_quant.log
-salmon/*/quant.genes.sf
-salmon/*/quant.sf
-salmon/salmon.*
+star_salmon/*.{bam,bam.bai}
+star_salmon/bigwig/*.{forward,reverse}.bigWig
+star_salmon/dupradar/box_plot/*_duprateExpBoxplot.pdf
+star_salmon/dupradar/histogram/*_expressionHist.pdf
+star_salmon/dupradar/scatter_plot/*_duprateExpDens.pdf
+star_salmon/featurecounts/*.featureCounts.txt.summary
+star_salmon/log/*.Log.{final.out,out,progress.out}
+star_salmon/picard_metrics/*.MarkDuplicates.metrics.txt
+star_salmon/qualimap/*/css/*
+star_salmon/qualimap/*/images_qualimapReport/*
+star_salmon/qualimap/*/qualimapReport.html
+star_salmon/qualimap/*/rnaseq_qc_results.txt
+star_salmon/rseqc/bam_stat/*.bam_stat.txt
+star_salmon/rseqc/read_distribution/*.read_distribution.txt
+star_salmon/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/*
+star_salmon/samtools_stats/*.bam.{flagstat,idxstats,stats}
+star_salmon/stringtie/*.ballgown/t_data.ctab
+star_salmon/stringtie/*.gene.abundance.txt
+star_salmon/stringtie/*.{coverage,transcripts}.gtf
 trimgalore/*fastq.gz_trimming_report.txt
+{salmon,star_salmon}/*/aux_info/fld.gz
+{salmon,star_salmon}/*/aux_info/meta_info.json
+{salmon,star_salmon}/*/libParams/flenDist.txt
+{salmon,star_salmon}/*/logs/salmon_quant.log
+{salmon,star_salmon}/*/quant.genes.sf
+{salmon,star_salmon}/*/quant.sf
+{salmon,star_salmon}/deseq2_qc/deseq2.dds.RData
+{salmon,star_salmon}/deseq2_qc/deseq2.pca.vals.txt
+{salmon,star_salmon}/deseq2_qc/deseq2.plots.pdf
+{salmon,star_salmon}/deseq2_qc/deseq2.sample.dists.txt
+{salmon,star_salmon}/deseq2_qc/size_factors/*.txt
+{salmon,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData
+{salmon,star_salmon}/salmon.*