Nextflow workflow report

[stoic_koch] (resumed run)

Run times

10-Jul-2026 10:48:44 - 10-Jul-2026 12:07:58 (duration: 1h 19m 14s)

  46 succeeded  

  26 cached  

  0 ignored  

  0 failed (10 retries)  

Nextflow command

nextflow run break-through-cancer/staple -r dev -profile igs --input samplesheet.csv --outdir /local/projects-t3/fertig_staple/osteosarc/staple/outs --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.h5ad --ref_scrna_type_col coarse_final_annot -w /usr/local/scratch/dlvovs/work --slurm_account ejfertig-lab -resume

CPU-Hours

28.9 (9% cached, 18.9% failed)

Launch directory

/autofs/projects-t3/fertig_staple/osteosarc

Work directory

/usr/local/scratch/dlvovs/work

Project directory

/home/dlvovs/.nextflow/assets/.repos/break-through-cancer/staple/clones/2c78896b813d2eb96f35b528001e1fdd8d38ceff

Script name

main.nf

Script ID

f4f72160b8480441912ea6c90a7d9cb2

Workflow name

STAPLE

Workflow version

2.3.0

Workflow description

Spot Transcriptomics Analysis Pipeline

Workflow home page

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

Workflow session

ab951f82-11c8-4381-aeb6-9113faf896e1

Workflow repository

https://github.com/break-through-cancer/staple, revision dev (commit hash 2c78896b813d2eb96f35b528001e1fdd8d38ceff)

Workflow profile

igs

Nextflow version

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