v1.2.8

Changelog

All notable changes to this project will be documented in this file.

[1.2.8] - 2025-03-19

Upgraded

• Variant caller: deepvariant:1.8.0
• Annotator: ensembl-vep:release_113.3
• Annotation source: Ensembl release 113 (Produces both RefSeq and Ensembl annoations)
• ClinVar: release 2025-03-12

Fixed

• Summary script to handle the updated VEP annotation fields.

[1.2.7] - 2024-10-11

Added

• Script to generate a summary table for depth of coverage per gene.

Updated

• Docker registry from DockerHub to GitHub to avoid DockerHub's rate limit restrictions.
• Dynamic runtime and bootdisk for handling PAPI error code 9.

[1.2.6] - 2024-06-24

Fixed

• Input to accept both fastq.gz and .fastq file format to the workflow.

[1.2.5] - 2024-02-19

Added

• Variant Filter based on QUAL > 30
• Filtered variants summary module now generates a variant-level summary .tsv file for all the variants based on the new filter criteria.
• VAF summary removed.

[1.2.4] - 2024-02-19

Added

• VEP annotation for structural variants.
• VEP annotated SV VCF to TSV -> Useful in filtering/sorting annotation data.
• Github Actions upgrade

[1.2.3] - 2024-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2024-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2024-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2024-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.7

Changelog

All notable changes to this project will be documented in this file.

[1.2.7] - 2024-10-11

Added

• Script to generate a summary table for depth of coverage per gene.

Updated

• Docker registry from DockerHub to GitHub to avoid DockerHub's rate limit restrictions.
• Dynamic runtime and bootdisk for handling PAPI error code 9.

[1.2.6] - 2024-06-24

Fixed

• Input to accept both fastq.gz and .fastq file format to the workflow.

[1.2.5] - 2024-02-19

Added

• Variant Filter based on QUAL > 30
• Filtered variants summary module now generates a variant-level summary .tsv file for all the variants based on the new filter criteria.
• VAF summary removed.

[1.2.4] - 2024-02-19

Added

• VEP annotation for structural variants.
• VEP annotated SV VCF to TSV -> Useful in filtering/sorting annotation data.
• Github Actions upgrade

[1.2.3] - 2024-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2024-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2024-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2024-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.6

Changelog

All notable changes to this project will be documented in this file.

[1.2.5] - 2022-02-19

Added

• Variant Filter based on QUAL > 30
• Filtered variants summary module now generates a variant-level summary .tsv file for all the variants based on the new filter criteria.#
• VAF summary removed.

[1.2.4] - 2022-02-19

Added

• VEP annotation for structural variants.
• VEP annotated SV VCF to TSV -> Useful in filtering/sorting annotation data.
• Github Actions upgrade

[1.2.3] - 2022-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2022-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.5

Changelog

All notable changes to this project will be documented in this file.

[1.2.5] - 2022-02-19

Added

• Variant Filter based on QUAL > 30
• Filtered variants summary module now generates a variant-level summary .tsv file for all the variants based on the new filter criteria.#
• VAF summary removed.

[1.2.4] - 2022-02-19

Added

• VEP annotation for structural variants.
• VEP annotated SV VCF to TSV -> Useful in filtering/sorting annotation data.
• Github Actions upgrade

[1.2.3] - 2022-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2022-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.4

Changelog

All notable changes to this project will be documented in this file.

[1.2.4] - 2022-02-19

Added

• VEP annotation for structural variants.
• VEP annotated SV VCF to TSV -> Useful in filtering/sorting annotation data.
• Github Actions upgrade

[1.2.3] - 2022-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2022-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.3

Changelog

All notable changes to this project will be documented in this file.

[1.2.3] - 2022-01-31

Added

• VEP annotated VCF to TSV -> Useful in filtering/sorting annotation data.

[1.2.2] - 2022-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.2

Changelog

All notable changes to this project will be documented in this file.

[1.2.2] - 2022-01-30

Fixed

• Coverage plot artifacts -> Sort coverage data by position

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.1

Changelog

All notable changes to this project will be documented in this file.

[1.2.1] - 2022-01-26

Fixed

• Summary module -> Improved file handling by checking if the input files exist and are non-empty before opening them.
• Summary module -> Added proper closing of file handles after reading the files.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.2.0

Changelog

All notable changes to this project will be documented in this file.

[1.2.0] - 2022-01-22

Added

• New depth of coverage plot with target genomic intervals.
• Added a new input param to the workflow region_to_plot which contains all the genomic coordinates of MTX1, GBAP1, MTX1P1 and GBA1.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp

v1.1.0

Changelog

All notable changes to this project will be documented in this file.

[1.1.0] - 2023-12-19

Added

• Added an additional summary of variants by applying a variant allele fractions (VAF) filter of greater than 0.5 to improve the confidence of the variants.

[1.0.0] - 2023-12-16

Added

• Initial release adapted from https://github.com/anand-imcm/wf-pb-amp