2.1.1

Bugs correction:

• major bug in dorado 0.8.0: "bug causing dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2 to
  call CpG contexts only and dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2 to call all contexts" (see https://github.com/nanoporetech/dorado/blob/release-v0.8/CHANGELOG.md#081-3-oct-2024).
• bug fix in snv filtering: filter was malformatted.
• remove ambiguity in wildcards between condition and paired samples for DMR

2.1.0

Input:

• Addition of UBAM (unaligned BAM) as alternative pipeline entrypoint. The available pipeline input files are now POD5, BAM and UBAM.

Steps modification:

• Fastq files Quality Control is now performed on the unaligned BAM file right after basecalling and before filtering (instead of the aligned BAM).
• All VCF files produced during the SNV annotation with SnpEff/SnpSift and CNV Calling with Spectre are now all bgzipped and indexed, it speeds up the following steps when compressed VCF files are accepted as input.
• By default, VCF files from SNV variant caller are first filtered to keep only the variants annotated as "PASS", before proceeding to the annotation step with SnpEff. "keep_only_pass" value was added in the config file to enable/disable this step when needed.

Miscellaneous:

• Addition of various verifications before running the pipeline (supplementary design and config files check, etc)
• Reads filtering parameters were added in the config file as "reads_filtering" value (default values: min read length = 1000 bp, min base quality score = 10 bp).
• Methylation content presence is now checked in UBAM and BAM files given as input of the pipeline if the user choses to perform any methylation analysis in his config file.
• SnpSift annotation rules were modified to ease various databases use.

Bugs correction:

• multiQC did not work correctly when 'basecalling_mode = basic' since it was searching for methylation output by default: a conditional input for multiQC was added, depending on wether methylation analysis is performed or not.
• Clair3 was not able to retrieve the input BAM index file since it was marked as temp() in the previous rule (reconcat_split_bam) and it was not given as an input to clair3 rule. It is now corrected.
• CuteSV sniffles2plot output were the same as the ones generated with Sniffles2 plot: wrong input path was corrected.
• Changed resources for modkit_pileup_uncomb rule as it returned some out of memory issues (even though it was labelled as a "Time Limit" error in slurm logs).

2.0.1

Analysis steps added:

• Preprocessing: Basecalling and Methylation calling
• Alignment
• Quality control (fastq, bam, methylation)
• Differential Methylated Regions (DMR) analysis between all samples and/or between two conditions
• Long Copy Number Variations (CNV) identification
• Phasing

Input:

• can be pod5 or aligned bam
• the format of the design file has changed
• we can give a file with interesting genes for maftools plots.

Reproducibility:

• Singularity images are pushed on zenodo instead of github.

Miscellaneous:

• Supplementary germline SV (cuteSV) and SNV (PEPPER-Margin-DeepVariant) variant callers were added for future consensus analysis.

1.0.0

First version of the pipeline: from bam to vcf, for germline or somatic analysis.