test: Maybe this was causing some deterministic issue

tests/.nftignore

@@ -17,6 +17,7 @@ pipeline_info/*.{html,json,txt,yml}
 */alignments/logs/*.txt
 star/log/*.Log.{final.out,out,progress.out}
 star/star/Log.out
+hisat2/log/*.hisat2.summary.log
 */deduplicated/logs/*.txt
 */{reports,summary}/*.{html,txt}
 **/*.command.log
@@ -34,91 +35,3 @@ transcript_identification/intersect/*_intersect.bed
 quality_control/bbsplit/*.stats.txt
 quality_control/**
 **/DupRate_plot.pdf
-
-hisat2/log/*.hisat2.summary.log
-kallisto/*/abundance.{h5,tsv}
-kallisto/*/kallisto_quant.log
-kallisto/*/run_info.json
-kallisto/kallisto.*
-pipeline_info/*.{html,json,txt,yml}
-sortmerna/*.sortmerna.log
-star_rsem/*.stat/*.{cnt,model,theta}
-star_rsem/*.{genes,isoforms}.results
-star_rsem/log/*.log
-star_salmon/log/*.Log.{final.out,out,progress.out}
-trimgalore/*fastq.gz_trimming_report.txt
-{hisat2,star_rsem,star_salmon}/*.{bam,bam.bai}
-{hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig
-{hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf
-{hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf
-{hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf
-{hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary
-{hisat2,star_rsem,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt
-{hisat2,star_rsem,star_salmon}/qualimap/*/css/*
-{hisat2,star_rsem,star_salmon}/qualimap/*/images_qualimapReport/*
-{hisat2,star_rsem,star_salmon}/qualimap/*/qualimapReport.html
-{hisat2,star_rsem,star_salmon}/qualimap/*/rnaseq_qc_results.txt
-{hisat2,star_rsem,star_salmon}/rseqc/bam_stat/*.bam_stat.txt
-{hisat2,star_rsem,star_salmon}/rseqc/read_distribution/*.read_distribution.txt
-{hisat2,star_rsem,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/*
-{hisat2,star_rsem,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats}
-{hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab
-{hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt
-{hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf
-{multiqc,multiqc/**}/multiqc_report.html
-{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
-{multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/hisat2_se_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
-{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
-{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc.log
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_data.json
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_hisat2.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_read_distribution.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_sortmerna.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt
-{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt
-{multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt
-{multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt
-{multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt
-{multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/rsem_multimapping_rates.txt
-{multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt
-{multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt
-{multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
-{multiqc,multiqc/**}/multiqc_report_data/rseqc_read_*.txt
-{multiqc,multiqc/**}/multiqc_report_data/salmon_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt
-{multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt
-{multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/sortmerna-detailed-plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt
-{multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt
-{multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
-{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.dds.RData
-{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.pca.vals.txt
-{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.plots.pdf
-{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt
-{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/*.txt
-{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData
-{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}/salmon.*