NaotoKubota/SnakeNgs: v0.4.0

[v0.4.0] - 2026-03-25 Added preprocessing_RNAseq_long.smk: Long-read RNA-seq preprocessing pipeline. preprocessing_CLIPseq.smk: Unified CLIP-seq preprocessing pipeline (HITS-CLIP, iCLIP-seq, etc.) with fastp_args, outFilterMultimapNmax, and normalize_bigwig config parameters. ONT_plasmid_assembly.smk: ONT sequencing data analysis for plasmid assembly. snakefile/common/containers.smk: Centralized Docker container definitions for all pipelines. snakefile/common/functions.smk: Shared utility functions (e.g., check_chromosome_length). GitHub Actions CI workflow for dry-run testing all Snakefiles on push/PR to develop. Changed preprocessing_RNAseq.smk: Merged preprocessing_RNAseq.smk and preprocessing_RNAseq_single.smk into a single file with layout config parameter ("paired" or "single"). Extracted common rules (sort, bigwig, makeRefFlat, makeRibosomalInterval, CollectRnaSeqMetrics) into snakefile/common/. Check chromosome lengths before indexing the bam file and make .csi index if a chromosome is over 512 Mbp. preprocessing_ChIPseq.smk: Merged preprocessing_ChIPseq.smk and preprocessing_ChIPseq_single.smk into a single file with layout config parameter ("paired" or "single"). Extracted common rules (sort, markdup, index, plotFingerprint, bigwig) into snakefile/common/. All Snakefiles: Centralized container definitions into snakefile/common/containers.smk using CONTAINERS["key"] references instead of hardcoded strings. All Snakefiles: Moved per-rule wildcard_constraints to workflow-level. Removed preprocessing_RNAseq_single.smk: Merged into preprocessing_RNAseq.smk. preprocessing_ChIPseq_single.smk: Merged into preprocessing_ChIPseq.smk. preprocessing_HITSCLIP.smk: Merged into preprocessing_CLIPseq.smk. preprocessing_iCLIPseq.smk: Merged into preprocessing_CLIPseq.smk.