Nextflow workflow report

[thirsty_feynman] (resumed run)

Run times

07-Oct-2026 08:02:25 - 07-Oct-2026 13:43:30 (duration: 5h 41m 5s)

  62 succeeded  

  16 cached  

  0 ignored  

  0 failed (1 retries)  

Nextflow command

nextflow run break-through-cancer/staple -r v2.5.0 -profile igs --input samplesheet.csv --outdir /local/projects-t3/fertig_staple/osteosarc/staple/outs-dropTCR-umi50-cellphone --xenium --deconvolve.n_top_genes 99999 --ref_scrna /local/projects-t3/fertig_staple/osteosarc/staple/072925_IPISRC044_T1_T2_T3_sobj_merged_processed_tcr_bcr_mutMap_tcMap_annot_final_reannot.h5ad --ref_scrna_type_col cell_type --slurm_account ejfertig-lab --drop_genes_prefix alpha,beta,epicentrx -w /local/scratch/dlvovs/work --sq_gr_co_occurrence_interval 50,100,150,200,250,300,350,400,450,500 --sq_gr_ligrec_interactions_params '{"resources": "CellPhoneDB"}' --umi_min 50 --analyze.spotlight Tumor -resume

CPU-Hours

160.1 (3.1% cached, 0.3% failed)

Launch directory

/autofs/projects-t3/fertig_staple/osteosarc

Work directory

/local/scratch/dlvovs/work

Project directory

/home/dlvovs/.nextflow/assets/.repos/break-through-cancer/staple/clones/8ae233d103a14775fd5f98424d75f67b67fda89d

Script name

main.nf

Script ID

f4f72160b8480441912ea6c90a7d9cb2

Workflow name

STAPLE

Workflow version

2.5.0

Workflow description

Spot Transcriptomics Analysis Pipeline

Workflow home page

https://github.com/break-through-cancer/staple

Workflow session

939dbae1-b720-4b41-a030-b24cf1872d66

Workflow repository

https://github.com/break-through-cancer/staple, revision v2.5.0 (commit hash 8ae233d103a14775fd5f98424d75f67b67fda89d)

Workflow profile

igs

Nextflow version

version 26.04.1, build 12112 (11-05-2026 13:29 UTC)