GitLab

Update frogs_w_fastidious_v5.pbs: remove _v5 in name, update ressources used to increase memory, replace outputmerge to output_merge so that dadamerge and frogs process can be run together successfully.

Update frogs.pbs: correct outputmerge to output_merge so that dadamerge and frogs process can be run together. Update pbs ressources to use mpi queue with 1 node incl. 28 cpus and 115g for faster processing. ATTENTION: FROGS may need up to 240g if using blast and rdp parallel assignment.

Update blast.pbs: set indir to output_merge when dada_mergeasv_process is activated so that dadamerge and blast process can be executed together

Update owi_renormalize.R: add ,quote = "\"" in read.table to better handle tab-delimited files, remove db[,(opt$end+1):ncol(db) to handle absence of columns after opt$end, remove obsolete column renaming

Replace dada2main.R: plotQualityProfile for 10 samples when possible, and truncQ=2 instead of truncQ=11

Replace frogs.pbs: frogs v2.0.0 (no fastidious) activating frogs-process independently AND after dada jobs, OR activating frogs-only independently AND after preprocessing jobs

Replace main.sh: updates of blast-assignation process to start independently as well, update of frogs-process to start independently as well

Replace config.sh, inlcudes following updates: bfrogs_fir changed to FROGS_dir, new numbering of output dirs, input_merge and output_merge explanations, frogs-process and frogs-only explanation

Update README.md: remove deprecated info, mention abyss-rename and frogs_only, better explain parameters 

Update README.md after last commit from Laure Quintric: mention abyss-rename for renaming sequence files, remove deprecated info.