test: Maybe this was causing some deterministic issue

nf-core · Dec 20, 2024 · 6f6af11 · 6f6af11
1 parent 828cad2
commit 6f6af11
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diff --git a/tests/.nftignore b/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.*
diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -329,6 +329,15 @@
                 "jurkat.minus.bigWig:md5,8a0ca6db6626d3fefb518f0d35dd1abc",
                 "jurkat.plus.bedGraph:md5,835edbd98f6d5d69e56de05e1a837b7c",
                 "jurkat.plus.bigWig:md5,66e82005e6c6730e970f7506bf93325c",
+                "cd4_REP1.sorted.bam.flagstat:md5,aa26d19a689b2fe97e254f125e1f7bcb",
+                "cd4_REP1.sorted.bam.idxstats:md5,d523e6e25ce8659871df4104dab503b0",
+                "cd4_REP1.sorted.bam.stats:md5,57b98494241870644c74edda7d503232",
+                "cd4_REP2.sorted.bam.flagstat:md5,6235482c2c1be02a23826261e2f8a033",
+                "cd4_REP2.sorted.bam.idxstats:md5,89de35c9f4f1eafa6944d5d574db1675",
+                "cd4_REP2.sorted.bam.stats:md5,aaa17a5a0018fa03cbadb1f5e354fa49",
+                "jurkat.sorted.bam.flagstat:md5,8e59ad91dd9df6003cb6c3070b0aa34c",
+                "jurkat.sorted.bam.idxstats:md5,56608a565532fc8ae2b93a3be28d5e8d",
+                "jurkat.sorted.bam.stats:md5,e100d7f3a79bb29ea3a99e610245e6c8",
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
@@ -355,6 +364,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-18T07:36:18.855708"
+        "timestamp": "2024-12-20T06:18:38.954985"
     }
 }