From 8776835e747aaf65a0dbf5f493e5154b32cdbd11 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 20 Dec 2024 13:24:33 +0100 Subject: [PATCH] fix erroneous addition of meta --- subworkflows/local/arriba_workflow/main.nf | 8 +- subworkflows/local/build_references.nf | 12 +- tests/test_stub.nf.test.snap | 431 ++++++++++++++++++++- 3 files changed, 432 insertions(+), 19 deletions(-) diff --git a/subworkflows/local/arriba_workflow/main.nf b/subworkflows/local/arriba_workflow/main.nf index bb4c36a6..5fa2ed2b 100644 --- a/subworkflows/local/arriba_workflow/main.nf +++ b/subworkflows/local/arriba_workflow/main.nf @@ -52,10 +52,10 @@ workflow ARRIBA_WORKFLOW { STAR_FOR_ARRIBA.out.bam, ch_fasta, ch_gtf, - ch_arriba_ref_blacklist.map{ it[1] }, - ch_arriba_ref_known_fusions.map{ it[1] }, - ch_arriba_ref_cytobands.map{ it[1] }, - ch_arriba_ref_protein_domains.map{ it[1] } + ch_arriba_ref_blacklist, + ch_arriba_ref_known_fusions, + ch_arriba_ref_cytobands, + ch_arriba_ref_protein_domains ) ch_versions = ch_versions.mix(ARRIBA_ARRIBA.out.versions) diff --git a/subworkflows/local/build_references.nf b/subworkflows/local/build_references.nf index 34102d2d..56fd8eb2 100644 --- a/subworkflows/local/build_references.nf +++ b/subworkflows/local/build_references.nf @@ -118,14 +118,10 @@ workflow BUILD_REFERENCES { ch_arriba_ref_known_fusions = ARRIBA_DOWNLOAD.out.known_fusions ch_arriba_ref_protein_domains = ARRIBA_DOWNLOAD.out.protein_domains } else { - ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { file -> - [ id: file.baseName, path: file ]} - ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { file -> - [ id: file.baseName, path: file ]} - ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { file -> - [ id: file.baseName, path: file ]} - ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { file -> - [ id: file.baseName, path: file ]} + ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist) + ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands) + ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions) + ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains) } diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index a60d6d13..e1892a6a 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -1,22 +1,343 @@ { "stub test no fastp trim": { "content": [ - 0, - null, + 29, + { + "ARRIBA_ARRIBA": { + "arriba": "2.4.0" + }, + "ARRIBA_DOWNLOAD": { + "arriba_download": "2.4.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FUSIONCATCHER": { + "fusioncatcher": 1.35 + }, + "FUSIONCATCHER_BUILD": { + "fusioncatcher": "fusioncatcher.py 1.35" + }, + "FUSIONREPORT": { + "fusion_report": "2.1.5" + }, + "FUSIONREPORT_DOWNLOAD": { + "fusion_report": "2.1.5" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.6.1.0" + }, + "GATK4_CREATESEQUENCEDICTIONARY": { + "gatk4": "4.6.1.0" + }, + "GATK4_MARKDUPLICATES": { + "gatk4": "4.5.0.0", + "samtools": "1.19.2" + }, + "GENCODE_DOWNLOAD": { + "wget": null + }, + "GET_RRNA_TRANSCRIPTS": { + "get_rrna_transcripts": "v1.0" + }, + "GFFREAD": { + "gffread": "0.12.7" + }, + "GTF_TO_REFFLAT": { + "gtfToGenePred": 377 + }, + "HGNC_DOWNLOAD": { + "wget": null + }, + "PICARD_COLLECTINSERTSIZEMETRICS": { + "picard": "3.3.0" + }, + "PICARD_COLLECTRNASEQMETRICS": { + "picard": "3.3.0" + }, + "SALMON_INDEX": { + "salmon": "1.10.3" + }, + "SALMON_QUANT": { + "salmon": "1.10.3" + }, + "SAMTOOLS_FAIDX": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX_FOR_STARFUSION": { + "samtools": 1.21 + }, + "STARFUSION": { + "STAR-Fusion": "1.14.0" + }, + "STARFUSION_BUILD": { + "STAR-Fusion": "1.14.0" + }, + "STAR_FOR_ARRIBA": { + "star": null, + "samtools": 1.2, + "gawk": "5.1.0" + }, + "STAR_FOR_STARFUSION": { + "star": null, + "samtools": 1.2, + "gawk": "5.1.0" + }, + "STAR_GENOMEGENERATE": { + "star": null, + "samtools": 1.2, + "gawk": "5.1.0" + }, + "STRINGTIE_MERGE": { + "stringtie": "2.2.1" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.3" + }, + "Workflow": { + "nf-core/rnafusion": "v4.0.0dev" + } + }, [ - + "arriba", + "arriba/test.arriba.fusions.discarded.tsv", + "arriba/test.arriba.fusions.tsv", + "fastqc", + "fastqc/test.html", + "fastqc/test.zip", + "fusioncatcher", + "fusioncatcher/human_v46", + "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt", + "fusioncatcher/test.fusioncatcher.fusion-genes.txt", + "fusioncatcher/test.fusioncatcher.log", + "fusioncatcher/test.fusioncatcher.summary.txt", + "fusionreport", + "fusionreport/test", + "fusionreport/test/AAA_BBB.html", + "fusionreport/test/test.fusionreport.tsv", + "fusionreport/test/test.fusionreport_filtered.tsv", + "fusionreport/test/test.fusions.csv", + "fusionreport/test/test.fusions.json", + "fusionreport/test/test_fusionreport_index.html", + "gatk4", + "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", + "get", + "get/rrna.bed", + "get/rrna.gtf", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "picard", + "picard/test.bai", + "picard/test.bam", + "picard/test.bam.metrics", + "picard/test.cram", + "picard/test.cram.crai", + "picard/test.rna_metrics", + "picard/test_collectinsertsize.pdf", + "picard/test_collectinsertsize.txt", + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/arriba", + "references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz", + "references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv", + "references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz", + "references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3", + "references/fusion_report_db", + "references/fusion_report_db/DB-timestamp.txt", + "references/fusion_report_db/cosmic.db", + "references/fusion_report_db/fusion_report.log", + "references/fusion_report_db/fusiongdb2.db", + "references/fusion_report_db/mitelman.db", + "references/gencode", + "references/gencode/Homo_sapiens.GRCh38.46.gtf", + "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", + "references/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", + "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", + "references/gffread", + "references/gffread/Homo_sapiens.GRCh38.46.gtf.fasta", + "references/hgnc", + "references/hgnc/HGNC-DB-timestamp.txt", + "references/hgnc/hgnc_complete_set.txt", + "references/salmon", + "references/salmon/salmon", + "references/salmon/salmon/complete_ref_lens.bin", + "references/salmon/salmon/ctable.bin", + "references/salmon/salmon/ctg_offsets.bin", + "references/salmon/salmon/duplicate_clusters.tsv", + "references/salmon/salmon/info.json", + "references/salmon/salmon/mphf.bin", + "references/salmon/salmon/pos.bin", + "references/salmon/salmon/pre_indexing.log", + "references/salmon/salmon/rank.bin", + "references/salmon/salmon/refAccumLengths.bin", + "references/salmon/salmon/ref_indexing.log", + "references/salmon/salmon/reflengths.bin", + "references/salmon/salmon/refseq.bin", + "references/salmon/salmon/seq.bin", + "references/salmon/salmon/versionInfo.json", + "references/star", + "references/star/Genome", + "references/star/Log.out", + "references/star/SA", + "references/star/SAindex", + "references/star/chrLength.txt", + "references/star/chrName.txt", + "references/star/chrNameLength.txt", + "references/star/chrStart.txt", + "references/star/exonGeTrInfo.tab", + "references/star/exonInfo.tab", + "references/star/geneInfo.tab", + "references/star/genomeParameters.txt", + "references/star/sjdbInfo.txt", + "references/star/sjdbList.fromGTF.out.tab", + "references/star/sjdbList.out.tab", + "references/star/transcriptInfo.tab", + "salmon", + "salmon/test", + "salmon/test_lib_format_counts.json", + "salmon/test_meta_info.json", + "star_for_arriba", + "star_for_arriba/test.Aligned.sortedByCoord.out.bam", + "star_for_arriba/test.Aligned.unsort.out.bam", + "star_for_arriba/test.Chimeric.out.junction", + "star_for_arriba/test.Log.final.out", + "star_for_arriba/test.Log.out", + "star_for_arriba/test.Log.progress.out", + "star_for_arriba/test.ReadsPerGene.out.tab", + "star_for_arriba/test.SJ.out.tab", + "star_for_arriba/test.Signal.UniqueMultiple.str1.out.bg", + "star_for_arriba/test.Signal.UniqueMultiple.str1.out.wig", + "star_for_arriba/test.out.sam", + "star_for_arriba/test.sortedByCoord.out.bam", + "star_for_arriba/test.tab", + "star_for_arriba/test.toTranscriptome.out.bam", + "star_for_arriba/test.unmapped_1.fastq.gz", + "star_for_arriba/test.unmapped_2.fastq.gz", + "star_for_arriba/testXd.out.bam", + "star_for_starfusion", + "star_for_starfusion/test.Aligned.sortedByCoord.out.bam", + "star_for_starfusion/test.Aligned.unsort.out.bam", + "star_for_starfusion/test.Chimeric.out.junction", + "star_for_starfusion/test.Log.final.out", + "star_for_starfusion/test.Log.out", + "star_for_starfusion/test.Log.progress.out", + "star_for_starfusion/test.ReadsPerGene.out.tab", + "star_for_starfusion/test.SJ.out.tab", + "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.bg", + "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig", + "star_for_starfusion/test.out.sam", + "star_for_starfusion/test.sortedByCoord.out.bam", + "star_for_starfusion/test.sortedByCoord.out.bam.bai", + "star_for_starfusion/test.tab", + "star_for_starfusion/test.toTranscriptome.out.bam", + "star_for_starfusion/test.unmapped_1.fastq.gz", + "star_for_starfusion/test.unmapped_2.fastq.gz", + "star_for_starfusion/testXd.out.bam", + "starfusion", + "starfusion/ctat_genome_lib_build_dir", + "starfusion/ctat_genome_lib_build_dir/AnnotFilterRule.pm", + "starfusion/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz", + "starfusion/ctat_genome_lib_build_dir/__chkpts", + "starfusion/ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/index_pfam_hits.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2.splice_bed.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2_genome_idx.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok", + "starfusion/ctat_genome_lib_build_dir/__chkpts/validate_ctat_genome_lib.ok", + "starfusion/ctat_genome_lib_build_dir/blast_pairs.dat.gz", + "starfusion/ctat_genome_lib_build_dir/blast_pairs.idx", + "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.gz", + "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.idx", + "starfusion/ctat_genome_lib_build_dir/pfam_domains.dbm", + "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa", + "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx", + "starfusion/ctat_genome_lib_build_dir/ref_annot.cds", + "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa", + "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx", + "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf", + "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans", + "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu", + "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed", + "starfusion/ctat_genome_lib_build_dir/ref_annot.pep", + "starfusion/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.mm2", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ndb", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nhr", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nin", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.njs", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.not", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nsq", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ntf", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nto", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab", + "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab", + "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat", + "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm", + "starfusion/ctat_genome_lib_build_dir/trans.blast.dat.gz", + "starfusion/test.starfusion.abridged.coding_effect.tsv", + "starfusion/test.starfusion.abridged.tsv", + "starfusion/test.starfusion.fusion_predictions.tsv", + "stringtie", + "stringtie/[:]", + "stringtie/[:]/stringtie.merged.gtf", + "stringtie/test.ballgown", + "stringtie/test.coverage.gtf", + "stringtie/test.gene.abundance.txt", + "stringtie/test.transcripts.gtf" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-20T11:51:44.033131" + "timestamp": "2024-12-20T13:17:20.018293" }, "stub test with fastp trim": { "content": [ - 18, + 31, { + "ARRIBA_ARRIBA": { + "arriba": "2.4.0" + }, "ARRIBA_DOWNLOAD": { "arriba_download": "2.4.0" }, @@ -35,12 +356,22 @@ "FUSIONCATCHER_BUILD": { "fusioncatcher": "fusioncatcher.py 1.35" }, + "FUSIONREPORT": { + "fusion_report": "2.1.5" + }, "FUSIONREPORT_DOWNLOAD": { "fusion_report": "2.1.5" }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.6.1.0" + }, "GATK4_CREATESEQUENCEDICTIONARY": { "gatk4": "4.6.1.0" }, + "GATK4_MARKDUPLICATES": { + "gatk4": "4.5.0.0", + "samtools": "1.19.2" + }, "GENCODE_DOWNLOAD": { "wget": null }, @@ -56,9 +387,27 @@ "HGNC_DOWNLOAD": { "wget": null }, + "PICARD_COLLECTINSERTSIZEMETRICS": { + "picard": "3.3.0" + }, + "PICARD_COLLECTRNASEQMETRICS": { + "picard": "3.3.0" + }, + "SALMON_INDEX": { + "salmon": "1.10.3" + }, + "SALMON_QUANT": { + "salmon": "1.10.3" + }, "SAMTOOLS_FAIDX": { "samtools": 1.21 }, + "SAMTOOLS_INDEX_FOR_STARFUSION": { + "samtools": 1.21 + }, + "STARFUSION": { + "STAR-Fusion": "1.14.0" + }, "STARFUSION_BUILD": { "STAR-Fusion": "1.14.0" }, @@ -67,16 +416,30 @@ "samtools": 1.2, "gawk": "5.1.0" }, + "STAR_FOR_STARFUSION": { + "star": null, + "samtools": 1.2, + "gawk": "5.1.0" + }, "STAR_GENOMEGENERATE": { "star": null, "samtools": 1.2, "gawk": "5.1.0" }, + "STRINGTIE_MERGE": { + "stringtie": "2.2.1" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.3" + }, "Workflow": { "nf-core/rnafusion": "v4.0.0dev" } }, [ + "arriba", + "arriba/test.arriba.fusions.discarded.tsv", + "arriba/test.arriba.fusions.tsv", "fastp", "fastp/test.fastp.html", "fastp/test.fastp.json", @@ -95,11 +458,32 @@ "fusioncatcher/test.fusioncatcher.fusion-genes.txt", "fusioncatcher/test.fusioncatcher.log", "fusioncatcher/test.fusioncatcher.summary.txt", + "fusionreport", + "fusionreport/test", + "fusionreport/test/AAA_BBB.html", + "fusionreport/test/test.fusionreport.tsv", + "fusionreport/test/test.fusionreport_filtered.tsv", + "fusionreport/test/test.fusions.csv", + "fusionreport/test/test.fusions.json", + "fusionreport/test/test_fusionreport_index.html", "gatk4", "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "get", "get/rrna.bed", "get/rrna.gtf", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "picard", + "picard/test.bai", + "picard/test.bam", + "picard/test.bam.metrics", + "picard/test.cram", + "picard/test.cram.crai", + "picard/test.rna_metrics", + "picard/test_collectinsertsize.pdf", + "picard/test_collectinsertsize.txt", "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "references", @@ -116,6 +500,7 @@ "references/fusion_report_db/mitelman.db", "references/gencode", "references/gencode/Homo_sapiens.GRCh38.46.gtf", + "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", @@ -124,6 +509,23 @@ "references/hgnc", "references/hgnc/HGNC-DB-timestamp.txt", "references/hgnc/hgnc_complete_set.txt", + "references/salmon", + "references/salmon/salmon", + "references/salmon/salmon/complete_ref_lens.bin", + "references/salmon/salmon/ctable.bin", + "references/salmon/salmon/ctg_offsets.bin", + "references/salmon/salmon/duplicate_clusters.tsv", + "references/salmon/salmon/info.json", + "references/salmon/salmon/mphf.bin", + "references/salmon/salmon/pos.bin", + "references/salmon/salmon/pre_indexing.log", + "references/salmon/salmon/rank.bin", + "references/salmon/salmon/refAccumLengths.bin", + "references/salmon/salmon/ref_indexing.log", + "references/salmon/salmon/reflengths.bin", + "references/salmon/salmon/refseq.bin", + "references/salmon/salmon/seq.bin", + "references/salmon/salmon/versionInfo.json", "references/star", "references/star/Genome", "references/star/Log.out", @@ -141,6 +543,10 @@ "references/star/sjdbList.fromGTF.out.tab", "references/star/sjdbList.out.tab", "references/star/transcriptInfo.tab", + "salmon", + "salmon/test", + "salmon/test_lib_format_counts.json", + "salmon/test_meta_info.json", "star_for_arriba", "star_for_arriba/test.Aligned.sortedByCoord.out.bam", "star_for_arriba/test.Aligned.unsort.out.bam", @@ -172,6 +578,7 @@ "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig", "star_for_starfusion/test.out.sam", "star_for_starfusion/test.sortedByCoord.out.bam", + "star_for_starfusion/test.sortedByCoord.out.bam.bai", "star_for_starfusion/test.tab", "star_for_starfusion/test.toTranscriptome.out.bam", "star_for_starfusion/test.unmapped_1.fastq.gz", @@ -252,13 +659,23 @@ "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab", "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat", "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm", - "starfusion/ctat_genome_lib_build_dir/trans.blast.dat.gz" + "starfusion/ctat_genome_lib_build_dir/trans.blast.dat.gz", + "starfusion/test.starfusion.abridged.coding_effect.tsv", + "starfusion/test.starfusion.abridged.tsv", + "starfusion/test.starfusion.fusion_predictions.tsv", + "stringtie", + "stringtie/[:]", + "stringtie/[:]/stringtie.merged.gtf", + "stringtie/test.ballgown", + "stringtie/test.coverage.gtf", + "stringtie/test.gene.abundance.txt", + "stringtie/test.transcripts.gtf" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-20T11:53:19.316547" + "timestamp": "2024-12-20T13:15:06.974011" } } \ No newline at end of file