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@MikeWLloyd MikeWLloyd released this 26 Sep 13:54
· 6 commits to main since this release
v0.7.3
b08c173

Release 0.7.3

In this release we make a updates to the ATAC workflow, and correct issues related to the PTA workflow.

ATAC:

  • Merging of replicate samples is now supported. Use the --merge_replicates option, along with a CSV input file. See the wiki page for details on CSV setup.
  • GRCm39 pseudo-references generated with G2Gtools are now supported. Previously, GRCm38 was supported via the --chain option. For GRCm39, VCI files are required input also specified with --chain

PTA:

  • The mouse PTA workflow would crash when all somatic CNVs were filtered, we have corrected this.
  • Numerous adjustments to adjustments to memory and wall clock limits were made to support high coverage WGS data.

Pipelines Added:

None

Modules Added:

  1. modules/g2gtools/g2gtools_vci_convert.nf

Pipeline Changes:

  1. workflows/atac.nf: Replicate merging added. GRCm39 pseudo-reference support added.
  2. subworkflows/aria_download_parse.nf: Support for replicate merging added.
  3. subworkflows/concatenate_local_files.nf: Support for replicate merging added.

Module Changes:

  1. modules/cosmic/cosmic_add_cancer_resistance_mutations_germline.nf: wallclock and memory request increase.
  2. modules/gridss/gridss_assemble.nf: memory request increase, and java heap adjustment.
  3. modules/gridss/gripss_somatic_filter.nf: memory request increase, and java heap adjustment.
  4. modules/illumina/manta.nf: memory and wallclock requests were made flat rather than scaled to input file size.
  5. modules/picard/picard_mergesamfiles.nf: correct file vs. path nextflow issue.
  6. modules/python/python_somatic_vcf_finalization.nf: wallclock requests increase.
  7. modules/python/python_somatic_vcf_finalization_mouse.nf: wallclock requests increase.
  8. modules/r/plot_delly_cnv.nf: add dynamic plot naming based on sampleID
  9. modules/samtools/samtools_chain_sort_fixmate_bam.nf: alter module to re-sort final filtered BAM prior to possible replicate merge.
  10. modules/samtools/samtools_non_chain_reindex.nf: alter module to re-sort final filtered BAM prior to possible replicate merge.
  11. modules/samtools/samtools_stats_insertsize.nf: wallclock request increase.
  12. modules/svaba/svaba.nf: memory and wallclock requests increase.

Scripts Added:

None

Script Changes:

  1. bin/gbrs/generate_emission_prob_avecs.py: Modify for use with non-DO strain IDs and dynamic number of strains.
  2. bin/pta/annotate-bedpe-with-cnv.r: Capture edge case where all somatic CNV are filtered.
  3. bin/pta/annotate-cnv-delly.r: Capture edge case where all somatic CNV are filtered.
  4. bin/pta/delly_cnv_plot.r: Capture edge case where all somatic CNV are filtered.

NF-Test Modules Added:

None

Assets 2
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