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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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.* |