sanger-tol/ascc: 0.5.0 - Red Spider-Boat

[0.5.0] - Red Spider-Boat [ ##/08/2024]

THIS IS STILL AN IN-DEVELOPMENT PROJECT SO THERE MAY BE BUGS.

Release 7 of sanger-tol/ascc, focusing on the 3.3.3 template upgrade and stability for sanger production.

Notes

• If running the pipeline in --profile singularity and you are crashing with a generic error, try using export NXF_SINGULARITY_NEW_PID_NAMESPACE=false.

Added

• Template update to 3.3.2.
• Added pipeline-level nf-test testing which is now running as standard CI.
• Corrected versioning in the .nextflow.log.
• Minor updates to the base.config.
• singularity pid setting is now false.
• Param to expose FILTER_FASTA ext.cutoff and enforce min/max values.
• The FCSGX module has been heavily patched when using --profile production, this is to support module and modulecmd.
• The --production profile now contains a FCSGX module override linked to the above. Resources have been included otherwise FCSGX will use the nextflow defaults.
• Changes to the resource allocation to improve support for large genomes. Changes are for the modules:
  • BLAST_BLASTN
  • BLAST_BLASTN_MOD
  • DIAMOND_BLASTX
  • TIARA_TIARA
  • MINIMAP2_ALIGN_SE
• Above changes also seperate out the logic for organellar genomes as they do not need the more complicated resource additions.
• Removed the BTK config, this has started to cause a number of crashes to the nested blobtoolkit pipeline.
• Remove unnecessary SAMTOOLS_INDEX from RUN_READ_COVERAGE.

Fixed

• Spelling mistakes... again.
• singularity pid env change is down to an issue with Singularity and FCSGX, multiple instances of the tool accessing the same DB files causes crashes.
• Correct value of 100Mb to 1Gb as the ext.cutoff for FILTER_FASTA
• GENERATE_SAMPLESHEET was only taking into account 1 read file for BTK rather than all provided read files.
• GENERATE_SAMPLESHEET was not using the reads_type variable.
• Changed instances of projectDir to launchDir for safety (In tests).
• Map pattern in ESSENTIAL_JOBS has been updated to reduce re-writing all values.
• Corrected references to withName: '*:PACBIO_BARCODE_CHECK:BLAST_BLASTN'.
• Updated resource notation to use e notation #134

Bugs

• Currently, Blobtoolkit will not run if there is no autofilter output channel.
• tiara, fcsgx, autofilter must always be activated.