Chore/docs and test cleanup#127
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…ME_REFERENCE Previously, params.protein_fasta was used for both GENCODE and custom protein FASTAs, causing header parsing failures when a custom/LRP FASTA was passed into the GENCODE slot (expected 8-field pipe-delimited headers). Changes: - Rename params.protein_fasta to params.custom_protein_fasta - Add params.lrp_protein_fasta for pre-computed LRP proteomes (proteomics-only runs) - GENCODE protein FASTA (pc_translations.fa) now auto-resolved from --genome via gencode_refs - BUILD_PROTEOME_REFERENCE module input tuple expanded from 4 to 5 elements (lrp_fasta, counts, custom_fasta, gencode_protein_fasta) - Each FASTA passed as named arg to R script (--lrp_fasta, --custom_fasta, --gencode_fasta) - GENCODE protein FASTA decompression gated on protein samples, not RNA samples - Add gencode_refs entries for v40-v42; fix v45 protein_fasta URL pointing to v46 - Fix FragPipe workflow file missing trailing newline (upstream Nesvilab #2730)
…flexible FASTA/GTF inputs to NOVEL_PEPTIDES Previously, peptide-to-genome BED mapping only ran when the full LRP pipeline was executed end to end. GENCODE and custom/LRP BED mapping now run independently based on their own inputs. - Replace --lr_cds_gtf/--lr_orf_fasta with --custom_fasta, --custom_gtf, --gencode_fasta, --gencode_gtf in novel_peptides.R and module - Add params.lrp_gtf and params.custom_gtf for proteomics-only runs - Fallback chain: pipeline output > --lrp_gtf/fasta > --custom_gtf/fasta (mirrors BUILD_PROTEOME_REFERENCE pattern)"
- Add LSF scheduler configuration. - Resolve FASTA database path inside container at runtime in FragPipe module. Path was previously resolved at Nextflow script generation time, which could produce a path not accessible inside the Apptainer/Singularity container. Switched to printf with $(pwd) for runtime resolution. - Replace heredoc with echo statements for versions.yml generation in FragPipe module to avoid indentation-sensitive parsing failures.
…ptional run parameters for slurm or lsf configs
…erence support, species-based hexamer model selection for CPAT, fix overwrite bug with RNA samples metadata for MULTISAMPLE_ANALYSIS triggered by running multiple datasets in same repository
…m value if provided, but otherwise ensure pipeline halts if user provides custom GTF and FASTA but does not set --species value
…sier run mode and suppression of second token being sent to user email when running on HPC
…exit status immediately fails pipeline (bypass issues related to module failing on HPC clusters but pipeline not terminating)
…STA for genome FASTA and GTF do not run when only protein samples with PROTEOMICS runs, modify channel setup in main workflow so that only RNA subworkflow processes shown in interactive mode when running with only RNA samples and vice versa with protein samples
…gtf and --gencode_fasta to --gtf and --fasta
…ollowing deprecated --fasta param removal, simplify container directives for isocall modules to avoid issue with unbound task variable when running with only singularity
…ing in user-friendly location
…king speedup proportional to cpus allocated, bump PROCESS_LONG tag up to 4 cpus by default to support chunking optimization
…long-running Fragpipe processes for large datasets
…input file details, example profile usage
…single-sample column naming to match multi-sample name format of FL.{sample_id}
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).