Changelog

Author: SeekGene

Time: 2 min

Words: 364 words

Updated: 2026-05-12

Reads: 0 times

All notable changes to this project will be documented in this file.

[2.1.2] 2026-04-30

Fixed

• Removed Fastp parameters --max-len1 60 --max-len2 0.
• Fixed several configuration issues.

[2.1.1] 2026-03-24

Fixed

• Resolved the input error "* Chromosome chrM doesn't present in the .genome file. *" in sc_methy_workflow.sh.

[2.1.0] 2026-03-13

Fixed

• Fixed an issue where batch FASTQ results were lost when forward and reverse fastq counts were unequal.

[2.0.0] 2026-02-26

Added

• Added a guide for building the reference genome database directory (--database_dir).
• Added a force_cell workflow for updating results based on previous outputs.
• Added validation for sample_id and outdir; whitespace is now disallowed and normalized to underscores.

Changed

• Optimized MCDS generation by splitting into smaller tasks and merging results.
• Updated repository layout documentation to match the current DSL2 structure.

[1.0.7] 2026-01-23

Fixed

• Fixed a bug in the step3 module where the allc_file_path.txt file was not being generated correctly.
• Updated sc_methy_workflow.sh to support multiple datasets per sample.

[1.0.6] 2025-12-30

Changed

• Updated nextflow.config.
• Updated methy_only.nf.
• Updated main.nf.

[1.0.5] 2025-12-22

Changed

• Updated barcode whitelist.

[1.0.4] 2025-12-18

Changed

• Updated the C-T conversion rate algorithm.

[1.0.3] 2025-12-09

Fixed

• Fixed a metric reporting issue in rna_methyl_report.html and rna_methy_summary.csv where values were incorrectly displayed as read numbers instead of read pairs (persisted in v1.0.1 and v1.0.2).

[1.0.2] 2025-12-02

Added

• Added a project parameter to tag each process with project-specific information.

Fixed

• Fixed a bug where cells containing only reverse reads or only forward reads were incorrectly filtered out.

[1.0.1] 2025-11-21

Changed

• Updated workflow version from 1.0.0 to 1.0.1 in nextflow.config.
• Updated the MET section in HTML reports to label and report values as "read pairs" instead of "reads".

Added

• Added a summary CSV file (rna_methy_summary.csv) containing the same metrics as the HTML report, saved in the same output directory.

[1.0.0] 2025-10-31

Added

• Initial release of the SeekSoul™ Methyl Tools pipeline for single-cell transcriptome and methylation dual-omics analysis.