clean nftignore for kallisto

Author: maxulysse

tests/.nftignore

@@ -1,125 +1,16 @@
-**/*DupRate_plot.{pdf,r}
-**/*Log.out
-**/*Log.{final,progress}.out
-**/*_fastqc.{html,zip}
-**/*_raw.{html,zip}
-**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg}
-**/*bam_stat.txt
-**/*coverage.gtf
-**/*fastq.gz_trimming_report.txt
-**/*featureCounts.txt.summary
-**/*gene.abundance.txt
-**/*hisat2.summary
-**/*inner_distance*
-**/*junction*
-**/*markdup.sorted.MarkDuplicates.metrics.txt
-**/*markdup.sorted.{bam,bam.bai}
-**/*read_distribution.txt
-**/*sorted.bam.{flagstat,idxstats,stats}
-**/*sortmerna.log
-**/*splice_{events,junction}.{pdf,png,svg}
-**/*transcripts.gtf
-**/*{cnt,model,theta}
-**/*{css,gif,js}
-**/*{forward,reverse}.bigWig
-**/*{genes,isoforms}.results
-**/*{pos,seq}.DupRate.xls
-**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt}
-**/Junction*.png
-**/Reads*.png
-**/abundance.{h5,tsv}
-**/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg}
-**/cutadapt_trimmed_sequences_*{pdf,svg}
-**/deseq2*
-**/dupradar-section-plot.{pdf,svg}
-**/fail_mapped_samples_table*
-**/fail_strand_check_table*
-**/fastqc-status-check-*{pdf,svg}
-**/fastqc_adapter_content_plot.{pdf,png,svg}
-**/fastqc_overrepresented_sequences_plot*{pdf,svg}
-**/fastqc_per_base_*_plot*{pdf,png,svg}
-**/fastqc_per_sequence_*{pdf,svg}
-**/fastqc_sequence_length_distribution_plot.{pdf,png,svg}
-**/fastqc_sequence_{counts,duplication_levels}_plot*{pdf,svg}
-**/fastqc_top_overrepresented_sequences_table*{pdf,png,svg,txt}
-**/featurecounts_biotype_plot-{cnt,pct}.{pdf,svg}
-**/fld.gz
-**/flenDist.txt
-**/general_stats_table.{pdf,png,svg}
-**/hisat2_pe_plot.txt
-**/hisat2_se_plot*{png,svg}
-**/hisat2_{pe,se}_plot-{cnt,pct}.{pdf,png,svg}
-**/junction_saturation_known.txt
-**/junction_saturation_novel.txt
-**/kallisto_alignment*{pdf,png,svg}
-**/kallisto_alignment.txt
-**/kallisto_quant.log
-**/meta_info.json
-**/multiqc_data.json
-**/multiqc_dupradar-section-plot.txt
-**/multiqc_fail_strand_check_table.txt
-**/multiqc_general_stats.txt
-**/multiqc_hisat2.txt
-**/multiqc_kallisto.txt
-**/multiqc_picard_dups.txt
-**/multiqc_plots
-**/multiqc_report.html
-**/multiqc_rsem.txt
-**/multiqc_rseqc_bam_stat.txt
-**/multiqc_rseqc_infer_experiment.txt
-**/multiqc_rseqc_junction_annotation.txt
-**/multiqc_rseqc_read_distribution.txt
-**/multiqc_salmon.txt
-**/multiqc_samtools_flagstat.txt
-**/multiqc_samtools_stats.txt
-**/multiqc_software_versions.txt
-**/multiqc_sortmerna.txt
-**/multiqc_sources.txt
-**/multiqc_star.txt
-**/multiqc_{salmon,star_salmon}_deseq2_pca-plot*txt
-**/picard_deduplication-{cnt,pct}.{pdf,png,svg}
-**/picard_deduplication.txt
-**/qualimapReport.html
-**/qualimap_gene_coverage_profile_Counts.{pdf,svg}
-**/qualimap_gene_coverage_profile_Normalised.{pdf,svg}
-**/qualimap_genomic_origin-{cnt,pct}.{pdf,png,svg}
-**/qualimap_genomic_origin.txt
-**/qualimap_rnaseq_genome_results.txt
-**/quant.genes.sf
-**/quant.sf
-**/rnaseq_qc_results.txt
-**/rsem_assignment_plot-{cnt,pct}.{pdf,png,svg}
-**/rsem_assignment_plot.txt
-**/rsem_multimapping_rates.{pdf,svg,txt}
-**/rseqc_bam_stat.{pdf,png,svg,txt}
-**/rseqc_infer_experiment_plot.{pdf,svg}
-**/rseqc_inner_*
-**/rseqc_junction_*
-**/rseqc_read_distribution_*
-**/rseqc_read_dups.txt
-**/rseqc_read_dups_plot.txt
-**/rseqc_read_dups_plot.{pdf,svg}
-**/run_info.json
-**/salmon_plot.{pdf,png,svg,txt}
-**/salmon_quant.log
-**/samtools-flagstat*
-**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Raw_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-stats-dp.{pdf,png,svg,txt}
-**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg}
-**/sortmerna-detailed-plot.txt
-**/star_summary_table.{pdf,png,svg,txt}
-**/t_data.ctab
-**/{kallisto,salmon}.merged*
-**/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg}
-**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg}
-**/{samtools,star}_alignment_plot*
-**/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg}
 bbsplit/*.stats.txt
+fastqc/*/*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/kallisto_alignment.txt
+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_software_versions.txt
+multiqc/multiqc_report_data/multiqc_sources.txt
+multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
 pipeline_info/*.{html,json,txt,yml}
-**/deseq2_qc/size_factors/*.txt
-star_rsem/log/*.log
+trimgalore/*fastq.gz_trimming_report.txt