1.7.3

[1.7.3] - 05/03/2026

Added

• scripts/submit_as_array.sh: Now works with the SLURM scheduler as well, for GRACE #36.
• scripts/run_Eager.sh:
  • Work directories renamed work -> temp #32.
  • Now works with the SLURM scheduler as well, for GRACE #36.
  • Inference of Library strandedness is now done based on the library protocol, instead of the sequencing run information.#34
• Added BL analysis type, for processing of Blanks.
• conf/Autorun.config: Added BL processing profile. Same as SG profile.

Fixed

Dependencies

Deprecated

• Removed monitoring of processing using Sequera platform/Nextflow tower #31.

1.7.2

[1.7.2] - 19/12/2025

Added

• scripts/prepare_eager_tsv.R: Added check for empty results tables before attempting to create TSVs. If no results are found for the specified sequencing batch and analysis type, a message is printed and no TSVs are created.

Fixed

Dependencies

Deprecated

1.7.1

[1.7.1] - 16/12/2025

Added

Fixed

• scripts/run_Eager.sh: Exclude hpc nodes from AE spawner job queue.
• scripts/ethical_sample_scrub.sh:
  • Remove existing directories if any.
  • Fixed warnings when TERM is unset.
• scripts/prepare_eager_tsv.R:
  • Now uses a direct SQL query to PandoraDB, which is faster and less resource-intensive than the old sidora.core call.
  • NAs are now allowed in the sequencing.Exclude column.

Dependencies

Deprecated

1.7.0

[1.7.0] - 15/08/2025

Added

• Singularity image build script for OSX systems using Docker.
• Singularity definition file for building the AE Singularity image.
• scripts/cron_daily_prepare.sh:
  • Now uses the new Singularity image sidora_AE_singularity.sif for running the prepare_eager_tsv.R script.
• scripts/update_poseidon_packages.sh:
  • Now uses the new Singularity image sidora_AE_singularity.sif for running the fill_in_janno.R and update_dataset_from_janno.R scripts.

Fixed

Dependencies

• Now requires the singularity image sidora_AE_singularity.sif, which can be built from the provided definition file and build script.

Deprecated

1.6.2

[1.6.2] - 29/07/2025

Added

• Processing of TM data. (1240k + mtDNA capture)

Fixed

• Corrected the AE version printed out by prepare_eager_tsv.R. Release 1.6.0 was incorrectly printed as 1.6.1.

Dependencies

Deprecated

1.6.0

[1.6.0] - 07/03/2025

Added

• Processing of YC data. (Y + mtDNA capture (YMCA))
• Processing of IM data. (Immunocapture)
• conf/Autorun.config:
  • Use hard links when publishing results, instead of copying files.
  • Add YC profile for processing YMCA data.
  • Add IM profile for processing Immunocapture data.
• scripts/create_poseidon_release.sh: New script to create large releases of the entire TF processed data in Poseidon format.
• Now compatible with Pandora Site IDs longer than 3 letters.
  • The following scripts can now infer Site_ID of varied lengths from the Ind_ID (pyPandoraHelper):
    • scripts/clear_results.sh
    • scripts/clear_work_dirs.sh
    • scripts/ethical_sample_scrub.sh
    • scripts/run_Eager.sh
    • scripts/update_poseidon_packages.sh
  • The following scripts can now infer Site_ID of varied lengths from the Ind_ID (rPandoraHelper):
    • scripts/prepare_eager_tsv.R
    • scripts/fill_in_janno.R
• Refactor how valid analysis types are determined in shell scripts, to make more easily extendable.
• scripts/prepare_eager_tsv.R:
  • Now uses Main_Individual_ID instead of Full_Individual_ID as the Sample_Name when one is provided.
  • Now excludes sequencing entries with the Exclude flag set to Yes.
• scripts/create_processed_ind_list.sh: Script to create a list of processed individuals across all analysis types, and a count of individuals in each analysis type.

Fixed

• scripts/run_Eager.sh: Java garbage collector now limited to one thread to avoid memory issues and hanging spawner jobs.

Dependencies

• pyPandoraHelper=0.2.1
• rPandoraHelper=0.2.0

Deprecated

1.5.0

[1.5.0] - 30/09/2024

Added

• Processing of RM data. (Twist capture + mtDNA)
  • conf/Autorun.config: Add RP profile for processing twist capture results. Identical to TF for now.
  • scripts/prepare_eager_tsv.R: Add RP analysis type for twist capture results
  • scripts/run_Eager.sh: Run for RP TSVs.
  • scripts/cron_daily_prepare.sh: Create RP analysis TSVs daily.
  • scripts/ethical_sample_scrub.sh: Add RP analysis type for ethical sample scrubbing.
  • scripts/clear_work_dirs.sh: Add RP analysis type for work directory clearing.
  • scripts/clear_results.sh: Add RP analysis type for results directory clearing.
• scripts/update_poseidon_packages.sh: Bump version for new release.
• README.md: Updated to list new state of the pipeline.

Fixed

Dependencies

Deprecated

1.4.0

Add processing of RP data.
Bump to nf-core/eager 2.5.0.
Use mapDamage with a read limit of 100k for damage calculations.

1.3.0

[1.3.0] - 12/07/2023

Added

• scripts/ethical_sample_scrub.sh: A script to remove eager input/outputs for samples that were marked as ethically sensitive after the pipelines picked them up.
• scripts/cron_ethical_scrub.sh: A cron-able script to run ethical_sample_scrub.sh daily.
• scripts/clear_work_dirs.sh: A bash script to rm -r the work directories of an individual ID for both SG and TF processing.
• scripts/clear_results.sh: A bash script that deletes the results for an individual while maintaining the nextflow process cache for them.

Fixed

• scripts/cron_daily_prepare.sh: Silenced permission errors due to ethical sample scrubbing.

Dependencies

Deprecated

1.2.0

[1.2.0] - 21/03/2023

Added

• prepare_eager_tsv.R: Added -w/--whitelist option. A whitelist of Pandora Individual IDs can be provided. Only the TSVs of individuals in the whitelist will be updated.

Fixed

• update_poseidon_packages.sh: Library_Names field now includes only unique library names.
• prepare_eager_tsv.R: Camel_Case versions of Pandora Analysis IDs are no longer filtered out.

Dependencies

Deprecated