atlas - Atlas Pipeline – Version [0.5.1]

Atlas Pipeline – Version [0.5.1]

Changelog

Conditional Execution for QCCalculator Output * Added a when: condition to the QCCalculator process to ensure it only runs when a valid output_folder is provided. * Prevents execution errors when the output folder is missing or empty in fastQSample mode. * Improves stability and flexibility when using optional output paths.

- Nextflow
Published by rolivella 9 months ago

atlas - Atlas Pipeline – Version [0.5]

Atlas Pipeline – Version [0.5]

Changelog

Added mzQC file support for Comet workflows (fastQSample mode only):

• In workflows using Comet and executing in fastQSample mode, the pipeline now:

  • Continues to generate the QC summary .tsv file.
  • Also generates a .mzQC file following HUPO-PSI specifications, using OpenMS QCCalculator.

• This improves compatibility with modern QC reporting tools and standard formats for raw-level quality control.

Designed to enhance traceability and interoperability of raw QC metrics across proteomics workflows.

---

Note: This feature is exclusive to fastQSample mode, where QC metrics are collected at the raw file level.

- Nextflow
Published by rolivella 10 months ago

atlas - Atlas Pipeline - Version [0.4]

📦 Atlas Pipeline - Version [0.4]

Changelog

• 🔧 Restructured configuration directories:

  • Clear separation into conf/, tools/, and assets/ for improved modularity and navigation.
  • Introduced SLURM profiles (tiny, small, medium, big) to allow flexible resource tuning per HPC environment.
  • ➕ More details available in the updated wiki section:
    👉 Configuration Files Location

• ⚙️ Added tool-specific configuration files:

  • New: tools/diann.config, tools/fragpipe.config, and tools/openms.config for cleaner separation of module-specific settings.

• 🧠 Improved flexibility and logic:

  • conf/slurm/slurm.config now supports dynamic QoS assignment based on runtime duration.
  • conf/shared.config consolidates global parameters like API URLs, Singularity settings, and paths.

• 📁 Assets and config files now better documented:

  • DIA-NN and FragPipe config files in assets/ are now included in the pipeline documentation.
  • ✅ Full config file documentation now available here:
    👉 Assets and Config Files Overview

This release improves maintainability, HPC adaptability, and provides detailed configuration documentation directly in the GitHub wiki.

- Nextflow
Published by rolivella 11 months ago

atlas - v.0.3

Atlas Pipeline - Version [0.3]

Changelog

• Updated DIA-NN to version 1.9.2.
  
• Added mzML file support for the DIA pipeline branch.
  
• Improved readability and structure of conf/defaultlab.config.
  
• Added Slack support for pipeline notifications.
  

This release improves compatibility, usability, and notifications.

- Nextflow
Published by rolivella about 1 year ago

atlas - v.0.2.2-alpha

Added support to Bruker TimsTOF for the DIA-NN branch of the pipeline (version 1.8.1).

- Nextflow
Published by rolivella over 1 year ago

atlas - v.0.2.1-alpha

• Added almost all metrics to TSV output file, in case it's configured.

- Nextflow
Published by rolivella over 1 year ago

atlas - v.0.2-alpha

• Added Fragpipe as a search engine, currently supporting only label-free workflows (not applicable to phosphoproteome, TMT, SILAC, etc.).
• Introduced a secondary reactions chart that shows the percentage of secondary reactions in the sample, represented as a percentage of the total peptide-spectrum matches (PSMs). This data is derived from identifications performed by Fragpipe using a closed search with specific mass shifts for secondary reactions. The chart is only available for DDA workflows.
• Added support for searching with existing predicted spectral libraries using DIA-NN.
• Removed support for DIA-Umpire.
• Performed code cleanup and optimization to manage JVM memory usage in the Fragpipe search process.

- Nextflow
Published by rolivella over 1 year ago

atlas - v.0.1.5-alpha Latest

Added counting generic modifications for SampleQC (Phospho TIO QC).

- Nextflow
Published by rolivella over 1 year ago

atlas - v.0.1.4-alpha

Fixed PTM counting algorithms and some bug fixes.

- Nextflow
Published by rolivella over 1 year ago

atlas - v.0.1.3-alpha

Highlighted feature: added mzsniffer (https://github.com/wfondrie/mzsniffer) for both DDA and DIA workflows.

- Nextflow
Published by rolivella almost 2 years ago

atlas - v.0.1.2-alpha

Added clitools docker: https://github.com/proteomicsunitcrg/atlas/commit/4352e044f0b6901c691734a0f25fc67107e2eceb Changed sample qc api keys: https://github.com/proteomicsunitcrg/atlas/commit/43504e0810889338ffd7f3ab3c0f10af3cddcb9c Fixed sample qc filenames: https://github.com/proteomicsunitcrg/atlas/commit/329270db346d8ce8fd26b40c7c9d731f97a3429d Added output folder for MQ and MK: https://github.com/proteomicsunitcrg/atlas/commit/befb01c172406de23880775ebc86c5053eff64eb

- Nextflow
Published by rolivella over 2 years ago

atlas - v.0.1.1-alpha

Fixed bug related to modification insertions to DB for Sample QC.

- Nextflow
Published by rolivella over 2 years ago

atlas - v.0.1.0-alpha

Reengineering for removing harcodes Reengineering of default lab methods for isolate them of test QC from our lab

For installing this pre-release, you should make a backup copy of the configuration files first. Then, just only replace your default_methods.csv for the new one.

- Nextflow
Published by rolivella over 2 years ago