Hey guys. I am running nf-core/mag for a project, and was wondering whether the -resume flag was working at all? I had to restart the job several times (and passed a new name, otherwise nf complains) but with the same work dir. It does not seem that nf-core/mag uses any of the previous results but instead runs all steps again. Is this a known thing? Am I doing something wrong? My command: nextflow run nf-core/mag \ -profile m3c \ -with-trace \ -with-dag "${OUTPUT_DIR}/flowchart_${NAME}_${ITERATION}.png" \ -with-report "${OUTPUT_DIR}/report_${NAME}_${ITERATION}.html" \ -name "${RUN_NAME}" \ -work-dir "${WORK_DIR}" \ -resume \ --input "${SAMPLESHEET}" \ --outdir "${OUTPUT_DIR}" \ --gtdb_db "$GTDBDB" \ --checkm2_db "$CHECKM2DB" \ --checkm_db "$CHECKMDB" \ --host_fasta "${HUMAN_GENOME}" \ --run_gunc \ --gunc_save_db

Hmmm, in principle no. I was using it last week with no issue. Note that if you give new names then it will restart from scratch - an annoyingly confusing/undocumented behaviour of nextflow is that if you use

-name ${RUN_NAME}

you need to replace it with

-resume {RUN_NAME}

... But otherwise I don't see any issues here, other than I don't know which version of the pipeline you are using! I would highly recommend pinning with

-r

the specific version

Ah... Alright ill try that. Guess i learned something new today :D