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Version 0.6.0 updates#58

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verku merged 59 commits intomainNBISweden/GenErode:mainfrom devNBISweden/GenErode:devCopy head branch name to clipboardJan 29, 2024

+991-902

Commits

Commits on Sep 15, 2023

• Update documentation

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• Replace rescale_gerp rule with -s parameter for gerpcol

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Commits on Sep 22, 2023

• Move scaling factor to compute_gerp rule so that the output is standardised but users can change the scaling directly in the rule

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• Clarify documentation

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• Clarify documentation about input tree and GERP score scaling

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Commits on Oct 4, 2023

• Fix typo

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  ec8b7ea

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• Update documentation

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• Integrate creation of chromosomal bed files into pipeline steps and update documentation

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• Add rule to remove sex chromosomes (optional) from merged VCF file and connect to pipeline

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Commits on Oct 5, 2023

• Implement sex chromosome removal from BCF files the same way as from mlRho to be compatible in a given pipeline run

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• Replace all with genome to be consistent with chr wildcard in 9_merge_vcfs.smk and to describe the file content better

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• Add genome for wildcard chr and constrain fmiss wildcard so that the BCF file can either be filtered for sex chromosomes (autos) or not (genome)

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• Implement running all downstream analyses with full genome-wide BCF files or with autosomal-only BCF files

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• Implement shorter way to select for genome-wide or autosomal-only BCF file

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• Update documentation

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Commits on Oct 6, 2023

• Add test to run part of pipeline without sex chromosomes

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• Remove *bai file from mlRho rule input to avoid triggering reruns of mappings because the *bai files are temporary files and because it is unnecessary

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• Update fastqc to version 0.12.1 to increase default memory allocation

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  dcc027e

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• Fix typo

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• Merge branch 'dev' into splitgenome

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• Merge branch 'gerp' into splitgenome

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• Update slurm configuration files with compute resources for new or changed rules

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• Move the filtering of individual BCF files from snpEff and GERP to 9_merge_vcfs.smk so that these rules are run only once if both steps are run

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• Run GERP for autosomes only if sex-chromosomal scaffold list is provided or for the whole genome if not

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• Update gitignore

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• Merge pull request #59 from NBISweden/gerp

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Commits on Oct 9, 2023

• Update to match pipeline config file and relax missingness filter

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  b3d6b33

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• Update pipeline version

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  8d9c521

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• Move stats output file to own directory for multiqc to only run on the specified filtering level

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• Merge branch 'dev' into splitgenome

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• Add missing wildcard to avoid that two or more jobs write to the same wildcard

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• Remove output files from all_outputs list that do not exist anymore

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Commits on Oct 10, 2023

• Describe average depth calculation more in detail

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Commits on Oct 11, 2023

• Update script to merge mlRho results for genome-wide analyses to match updated file names

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Commits on Oct 12, 2023

• Add runtime to rules in slurm config file that was missing

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• Make sure missingness_filtered_vcf_multiqc is also run on historical or modern samples only

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• Merge branch 'dev' into splitgenome

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• Add missing expand() function to collect output files from multiqc

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• Merge branch 'dev' into splitgenome

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  d12ff2d

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• Merge branch 'main' into dev

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• Merge branch 'dev' into splitgenome

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Commits on Oct 13, 2023

• Add MultiQC files for merged and filtered VCF files to the pipeline report

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Commits on Oct 17, 2023

• Merge pull request #57 from NBISweden/splitgenome

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• Update repeatmodeler to version 2.0.4 to handle large genomes

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• Add Github action Free Disk Space (Ubuntu) to free some disk space between setting up singularity and conda and running GenErode

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• Copy the repeat library from the updated repeatmodeler container

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• Remove parameter pointing to RepeatMasker installation that wrongly pointed to RepeatMasker libraries

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• Remove rule that copies RepeatMasker library as this does not seem to be required in the new container

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• Remove repeatclassifier rule to test if the final output is generated by the latest repeatmodeler version

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• Update repeatmodeler parameter according to container version

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Commits on Oct 24, 2023

• Merge pull request #63 from NBISweden/repeatmodeler

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Commits on Oct 25, 2023

• Remove temporary flag from merged vcf to avoid triggering a re-run of merging when testing different filtering levels for missingness

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• Remove copying the repeatmask bed file to reduce file number and triggering reruns of downstream rules

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• Skipping extracting modern or historical samples from merged and filtered VCF file when the pipeline is only run for modern or historical samples, respectively, avoiding generation and storage of d…

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• Update function to collect the correct input files for multiqc so that extraction of historical or modern samples is avoided when running the pipeline for only historical or only modern samples

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Commits on Oct 31, 2023

• Return to solution to extract modern or historical samples even when only run for one dataset

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Commits on Nov 14, 2023

• Add Xmx option to use allocated memory more efficiently

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Commits on Jan 17, 2024

• Remove flag -a that creates *.fasta.align file in RepeatMasker since this file is not required

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• Remove rule that has been removed from workflow

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