Spectronaut-nf v2.8.0

New

• Users can generate an image file (docker or HPC compatible .sif) from Spectronaut debian. The defination file - Dockerfile or spectronaut.def can be used to generate these images as described in the documentation container_README.md.
• Users can also run this version of the pipeline using the native linux compatible Spectronaut (SpectronautCMD.dll).
• Added a document describing the guidelines for future contributions.

Changed

• Reorganised the Spectronaut container build materials under Container/, replacing the earlier Container_Image_Setup/ location.
• Updated the container build definition to install the .NET 8 SDK and a supplied Spectronaut Debian package.
• Updated container documentation with Apptainer/Singularity and Docker build, test, and conversion instructions, including notes for WSL2.
• Retained the Nextflow workflow changes from v2.7.0; main.nf is unchanged between the v2.7.0 and v2.8.0 tags.

Spectronaut-nf v2.1.0

• Updated README for better user understanding of input parameters required and output folder generated by the pipeline.
• Users can define the maximum number of SNE files to be used for SNE merging.

Spectronaut-nf v2.0.0

• Works with Spectronaut version > 20.4
• The pipeline does a 3 stage Pulsar search, which results in more consistent IDs across different platforms (ex: Windows, Single Node and Multi-Node HPC)
• Now users can provide/set the input parameters in a user friendly params.yaml file

Spectronaut-nf v1.0.0

• Works only with Spectronaut version < 20.0
• Random sampling: spectral library generation from user defined sample size
• Batch processing: Multiple raw files can be subjected to single library generation and DIA searches – improved run time
• Raw file exclusion option: exclusion of raw files based on a specific pattern for DIA search
• Other inputs: Search parameters (.prop), conditions table (.tsv) and report template (.rs)