Code

Updates for GenErode version 0.6.1#82

Code

Merged

verku merged 47 commits intomainNBISweden/GenErode:mainfrom devNBISweden/GenErode:devCopy head branch name to clipboardJun 19, 2024

+1,589-368

Commits

Commits on Mar 25, 2024

• Add a Snakemake pipeline to process snpEff output for potential and realised load calculations

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  9ade8e5

Commits on Mar 26, 2024

• Add documentation on configuration of slurm profile

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  46cbe33

Commits on Apr 2, 2024

• Add resources for new rule

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  d60d260

Commits on Apr 22, 2024

• Add automatic calculation of memory for java tools

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  28f782a

• Adjust computational requirements to larger dataset

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  7c77350

Commits on May 15, 2024

• Update computational resources for larger datasets

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  2033626

Commits on Jun 14, 2024

• Update to snakemake version 8

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  ef4517e

• Fix syntax warning by adding escape characters

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  ada3e0b

• Update slurm config files

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  381dc23

• Switch to qualimap version 2.3

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  5c78406

• Switch to seqera singularity container

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  cee9004

• Undo double escape characters in regular expression due to syntaxwarning

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  654f4b5

• Add resources specific to rules and groups

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  d73f649

• Prefix the string with r so that Python treats the string as a raw string so that escape sequences will not be processed

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  801fd7d

• Switch to version 1.20 from seqera

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  1e9a163

• Remove deprecated command line option to print reasons for rule execution

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  4769cab

• Add a README with instructions on how to run GenErode with the slurm plugin. To be moved to the WIKI with the release of the next version

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  b69bac9

Commits on Jun 16, 2024

• Replace sequera container with galaxyproject container for bcftools 1:20

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  0639bad

• Update documentation

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  5d53485

• Add flag -k to keep going when a job fails until none of the jobs can be started anymore

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  9df5bc6

• Switch back to bcftools 1.19

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  d784a84

• Update compute resources

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  4caeb02

• Add snakemake executor plugin slurm to GenErode conda environment

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  5f31057

Commits on Jun 17, 2024

• Switch back to bcftools 1.20 from the galaxy project

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  201ecd5

• Update calculation of mem to provide to tools based on mem_mb specified in resources or slurm plugin config.yaml

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  a57ada1

• Add separate config files for Dardel and Rackham

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  9f7b9b3

• Add set-threads section back to config.yaml for slurm plugin

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  edb1a28

• Remove flag -m

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  1563a35

• Remove path to temporary directory

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  3c437dc

• Switch to sequera container and upgrade to version 1.4

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  4fa505a

• Switch to galaxyproject container

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  bca2e56

• Replace plink container with galaxyproject container and switch to version 1.90b6.21

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  09b02a2

• Update the README file according to latest changes made to the repository

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  57f3ba5

• Specify threads in rule

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  e6598cc

• Switch back to same version as before but from galaxy project

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  150c604

Commits on Jun 18, 2024

• Update the readme for slurm profiles

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  bc89adf

• Clarify compute resource specifications in current configuration file

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  cb95f67

• Relaxed depth filters to get more SNPs for test runs

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  248d623

Commits on Jun 19, 2024

• Merge pull request #80 from NBISweden/snakemake8

  Show description for 1a72e6c
  verku

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  1a72e6c

• Update formatting

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  bea4f5f

• Switch to Dardel's long partition for shorter wait time in queue

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  d87b46b

• Fix yaml format

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  93b5e88

• Fix mapping of threads with config.yaml for Dardel and Rackham using the slurm executor plugin

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  1f3f453

• Merge pull request #81 from NBISweden/snakemake8

  Show description for f83b944
  verku

  authored
  f83b944

• Update configuration files for slurm executor plugin profiles

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  a803dc4

• Move general instructions to WIKI

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  f842973

• Merge pull request #83 from NBISweden/snakemake8

  Show description for 144939a
  verku

  authored
  144939a