Work Directory

Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1)
Attempt
1
S3 Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/e928397933318d30a4344e8c6f0121

Files (108)

Name Size Modified
.command.begin 6 bytes Jun 08, 2026 2:51 AM
.command.err 4.9 KB Jun 08, 2026 4:13 AM
.command.log 40.9 KB Jun 08, 2026 4:13 AM
.command.out 35.1 KB Jun 08, 2026 4:13 AM
.command.run 14.4 KB Jun 08, 2026 2:51 AM
.command.sh 690 bytes Jun 08, 2026 2:51 AM
.command.trace 294 bytes Jun 08, 2026 4:13 AM
.command.yaml 3.9 KB Jun 08, 2026 2:51 AM
.exitcode 1 byte Jun 08, 2026 4:13 AM
FusionInspector.log 45.0 KB Jun 08, 2026 4:13 AM
HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv 1.1 KB Jun 08, 2026 4:13 AM
HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 5.0 KB Jun 08, 2026 4:13 AM
HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.FusionInspector.fusions.tsv 32.1 KB Jun 08, 2026 4:13 AM
HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_inspector_web.html 49.6 KB Jun 08, 2026 4:13 AM
chckpts_dir/EM_adj_counts.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.bed.bedsort.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.bed.bgzip.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.bed.tabix.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.junction_reads.bam.bedsort.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.junction_reads.bam.bgzip.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.junction_reads.bam.tabix.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.spanning_reads.bam.tabix.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/add_FFPM.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/add_splice_info.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/annot_filter.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/append_microH_info.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/blast_filter.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/coalesce_junc_n_span.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/cp_consol_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/cp_contigs_file_workdir 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/cp_final.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/cp_gtf_file_workdir.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/create_fi_igvjs.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/cytoband.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/filter_by_frag_threshs.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/final.abridged.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/fusion_annotator.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/fusion_coding_region_effect.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/fusion_contigs.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/fusion_reports_html.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/index_consol_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/init_EM_adj_counts.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/init_spanning_reads_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/mark_dup_reads.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/mark_dups_reads.index.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/merged_contig_fai.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/merged_contig_gtf_to_bed.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/microH.dat.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_extract_junc_reads.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_junc_reads_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_juncspan_fmt.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_pfam_bed.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_pfam_gff3.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_sam_frag_coordss.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_seqsim_bed.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_igv_seqsim_gff3.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/prep_spanning_reads.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/run_STAR.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/samtools_idx_junc_reads_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/samtools_index_span_reads_bam.ok 0 bytes Jun 08, 2026 4:13 AM
chckpts_dir/span_reads_acc.ok 0 bytes Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fa 26.7 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary 34.3 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj 34.4 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 31.8 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 32.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter 32.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.info 32.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter 32.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter.info 32.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 21.7 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 293 bytes Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.gtf 65.1 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam 578.5 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.bai 1.9 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.failed_reads_during_span_analysis 131.1 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 218.9 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info 22.2 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 0 bytes Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 12.7 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.read_align_counts.idx 2.1 MB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.read_align_counts.idx.ok 0 bytes Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.spanning_reads_want.idx 8.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.sortedByCoord.out.bam 921.2 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.sortedByCoord.out.bam.bai 2.0 KB Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.sortedByCoord.out.bam.bai.ok 0 bytes Jun 08, 2026 4:13 AM
fi_workdir/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.star.sortedByCoord.out.bam.ok 0 bytes Jun 08, 2026 4:13 AM
fi_workdir/Log.final.out 2.0 KB Jun 08, 2026 4:13 AM
fi_workdir/Log.out 20.2 KB Jun 08, 2026 4:13 AM
fi_workdir/Log.progress.out 7.8 KB Jun 08, 2026 4:13 AM
fi_workdir/SJ.out.tab 10.3 MB Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/exonGeTrInfo.tab 1.8 KB Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/exonInfo.tab 837 bytes Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/geneInfo.tab 124 bytes Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/sjdbInfo.txt 10.8 MB Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/sjdbList.fromGTF.out.tab 547 bytes Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/sjdbList.out.tab 9.5 MB Jun 08, 2026 4:13 AM
fi_workdir/_STARgenome/transcriptInfo.tab 963 bytes Jun 08, 2026 4:13 AM
fi_workdir/microH.dat 1.8 KB Jun 08, 2026 4:13 AM
fi_workdir/pipeliner.1149.cmds 1.0 KB Jun 08, 2026 4:13 AM
fi_workdir/star_align.ok 0 bytes Jun 08, 2026 4:13 AM
versions.yml 103 bytes Jun 08, 2026 4:13 AM