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Clinical-Genomics/oncoflow: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0.0dev - [unreleased]

Initial release of Clinical-Genomics/oncoflow, created with the nf-core template.

Added

  • #2 Added NEXTFLOW_RUN local module based on mahesh-panchal/nf-cascade.
  • #3 Added NFCORE_ONCOANALYSER using the NEXTFLOW_RUN local module to run the nf-core/oncoanalyser pipeline in ONCOFLOW workflow.
  • #3 Added input parameters for running nf-core/oncoanalyser: oncoanalyser_config, oncoanalyser_nextflow_opts and oncoanalyser_samplesheet.
  • #5 and #10 Added CREATE_PARAMS_FILE local module.
  • #9 CREATE_ONCOANALYSER_PARAMS_FILE using CREATE_PARAMS_FILE to ONCOFLOW workflow.
  • #9 Added input parameters oncoanalyser_create_stub_placeholders, oncoanalyser_genome and oncoanalyser_mode necessary for creating the oncoanalyser params file using the CREATE_ONCOANALYSER_PARAMS_FILE local module.
  • #9 getOncoanalyserParamsList function to produce the list of parameters necessary for CREATE_ONCOANALYSER_PARAMS_FILE.
  • #5 and #10 Added CREATE_ONCOREFINER_PARAMS_FILE using CREATE_PARAMS_FILE to ONCOFLOW workflow.
  • #5 Added metadata parameters case_id, sample_id_tumor, sample_id_normal, subject_id and sex, necessary for creating the oncorefiner params file using the CREATE_ONCOREFINER_PARAMS_FILE local module.
  • #10 Added getOncorefinerParamsList function to produce the list of parameters necessary for CREATE_ONCOREFINER_PARAMS_FILE.
  • #4 Added CLINICAL_GENOMICS_ONCOREFINER using the NEXTFLOW_RUN local module to run the Clinical-Genomics/oncorefiner pipeline in ONCOFLOW workflow.
  • #4 Added input parameters for running Clinical-Genomics/oncorefiner: oncorefiner_config and oncorefiner_nextflow_opts.
  • #17 Added linx_fusion_tsv, linx_breakends_tsv and linx_sv_tsv parameters to getOncorefinerParamsList.
  • #30 Added amber_baf_tsv_gz, cobalt_ratio_pcf_normal, cobalt_ratio_pcf_tumor, cnv_gene_tsv, cnv_segment_tsv parameters to getOncorefinerParamsList.

Changed

  • #3 Changed default test to not capture pipeline_info files for all pipelines.
  • #3 and #4 Updated .nftignore to ignore pipeline_info, multiqc and vep files for all pipelines.
  • #3 Updated .nftignore to ignore gzipped output files from oncoanalyser due to nf-core/oncoanalyser#299.
  • #3 Updated .nftignore to ignore *.command.* output files from oncoanalyser since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot.
  • #8 Changed NFCORE_ONCOANALYSER to run forked fixed Clinical-Genomics/oncoanalyser instead, due to bug nf-core/oncoanalyser#301.
  • #8 Changed test config to run the above with revision 2.2.0-with-purple-tbi-fix which includes the fix for nf-core/oncoanalyser#301 and nf-core/oncoanalyser version 2.2.0 since this was the version used for previous test runs.
  • #11 Set process.errorStrategy = 'finish' for all processes to allow for resuming runs after there is an error while running a pipeline.
  • #13 Changed logic to propagate the oncoflow config file for all run pipelines but also allow for providing individual config files for each pipeline through the corresponding parameters.
  • #19 Set revision for oncorefiner in test config.
  • #18 Updated test config to use the revised oncoanalyser version 2.2.0-with-purple-and-linx-stub-fix.
  • #21 Updated test config to use latest dev revision of oncorefiner.
  • #22 Removed logic to propagate config file to child pipelines.
  • #23 Updated test config to use oncoanalyser version 3.0.0 - patched revision 3.0.0-with-linx-stub-fix - and compatible oncorefiner version - revision d876cc0b576892210bc52c1486c3eec3d3aaa1de.
  • #23 Updated bam file paths in getOncorefinerParamsList for compatibility with updated output file structure of oncoanalyser version 3.0.0.
  • #24 Updated the nextflow version from 25.10.4 to 26.04.0.
  • #25 Updated NEXTFLOW_RUN local module based on fix from mahesh-panchal/nf-cascade#6, to ensure compatibility with running with Nextflow Tower.
  • #26 Updated NEXTFLOW_RUN module to sync with new version from mahesh-panchal/nf-cascade.
  • #25 Updated NEXTFLOW_RUN local module to ensure compatibility with running with Nextflow Tower with the current Hasta nextflow config.
  • #28 Updated file paths for Oncoanalyser collection to use case_id and sample_id_tumor/normal. Also updated meta information to match the test data from Oncoanalyser.
  • [#29][#29] Updated test config to use oncoanalyser version 3.0.0 - patched revision 3.0.0-with-linx-cobalt-amber-stub-fix .
  • #31 Updated documentation.

Fixed

Dependencies

Deprecated