. . . . "config.yml" . "samples: samples.csv\n\nref:\n species: \"Drosophila melanogaster\"\n genome: \"\"\n annotation: \"\"\n accession: \"GCF_000001215.4\"\n ensembl_species: \"\" # e.g., \"homo_sapiens\"\n build: \"\" # e.g., \"GRCh38\"\n release: \"\" # e.g., \"105\"\n\nread_filter:\n min_length: 200\n\nminimap2:\n index_opts: \"\"\n opts: \"\"\n maximum_secondary: 100\n secondary_score_ratio: 1.0\n\nsamtools:\n samtobam_opts: \"-b\"\n bamsort_opts: \"\"\n bamindex_opts: \"\"\n bamstats_opts: \"\"\n\nquant:\n salmon_libtype: \"U\"\n\ndeseq2:\n fit_type: \"\"\n design_factors:\n - \"condition\"\n lfc_null: 1.0\n alt_hypothesis: \"greaterAbs\"\n point_width: 20\n mincount: 10\n alpha: 0.05\n threshold_plot: 10\n colormap: \"Blues\"\n figtype: \"png\"\n batch_effect:\n - \"\"\n\nisoform_analysis:\n FLAIR: true\n qscore: 1\n exp_thresh: 10\n col_opts: \"--annotation_reliant generate --generate_map --stringent\"\n\nprotein_annotation:\n lambda: false\n uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"\n num_matches: 3" . . "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.\nFirst a transcriptome FASTA is constructed using gffread [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2].\nNext quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2].\nThe workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow.\nAdditionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results." . "2026-04-17T14:23:10.537850+00:00"^^ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "alignment_qa" . . "alignment_qa_report" . . "alignment_qa_report" . . "alignment_qa_report" . . "bam_sort" . . "bam_sort" . . "bam_sort" . . "bam_sort" . . "bam_sort" . . "bam_sort" . . "bam_stats" . . "alignment_qa" . . "bam_stats" . . "bam_stats" . . "bam_stats" . . "bam_stats" . . "bam_stats" . . "build_flair_genome_index" . . "build_minimap_index" . . "correct_transcriptome" . . "count_reads" . . "count_reads" . . "alignment_qa" . . "count_reads" . . "count_reads" . . "count_reads" . . "count_reads" . . "deseq2" . . "deseq2_init" . . "download_ncbi_annotation" . . "download_ncbi_genome" . . "filter_reads" . . "filter_reads" . . "alignment_qa" . . "filter_reads" . . "filter_reads" . . "filter_reads" . . "filter_reads" . . "flair_align" . . "flair_collapse" . . "flair_correct" . . "flair_diffexp" . . "flair_plot_isoforms" . . "flair_quantify" . . "alignment_qa" . . "genome_to_transcriptome" . . "get_annotation" . . "get_genome" . . "gff_to_gtf" . . "iso_analysis_report" . . "map_reads" . . "map_reads" . . "map_reads" . . "map_reads" . . "map_reads" . . "alignment_qa" . . "map_reads" . . "merge_read_counts" . . "reads_manifest" . . "sam_to_bam" . . "sam_to_bam" . . "sam_to_bam" . . "sam_to_bam" . . "sam_to_bam" . . "sam_to_bam" . . "sample_qa_plot" . . "alignment_qa_report" . . "sample_qa_plot" . . "sample_qa_plot" . . "sample_qa_plot" . . "sample_qa_plot" . . "sample_qa_plot" . . "standardize_gff" . . "total_sample_qa_plot" . . "transcriptid_to_gene" . . "alignment_qa_report" . . "alignment_qa_report" . "from workflow configuration" . . "2026-04-17T16:23:11.855128"^^ . . "2026-04-17T14:23:10.537850+00:00"^^ . . . . "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "2026-04-17T16:23:11.855128"^^ . . "RSA" . "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB" . "RWZ3dlsLBdw7Q0vAkQ6lXqIqXWIV/DUMp7moQ9Dswbxq17j9DHlrFn5Vvun/ihdDmq0786J8XXIvP0D+L4/7cc2dWfayRFx4wL1GxdHvxxzIK/UqiZmQLyB9d1k2tpTvcni8VYYsUYw6uXgkoSkZSHR81m2XqqRrCgbvfdfn/x1qhmKYpzNrGosUMAQTW44UElZJLjoCdRTFiccPZRTGJC1F6GYaqxmdPv/IYBI7jQNeKL2CcPhDojYCjiIifn3QUQ/Qpdfe1HagB3xGtXspo5JRgzn/f5cwECf2KZGRYGonnshrN3CZri16UI7PKCKK4hSyzGol4ZN7gi5z2DIFZA==" . . .