How to skip rerunning tasks that have already been completed when using the -resume parameter?

[lihuacao007]

Description of the bug

Dear Developer,
Hello. I encountered the following issue when using nf-core/sarek to analyze my WES data (human, tumor and paired normal samples):

I first processed a batch of samples. After the tasks completed successfully, I added some new samples by modifying the samplesheet.csv file. However, when I ran the pipeline again, I found that the analyses for the first batch of already-completed samples were still being re-executed (e.g., BWA MEM), as shown in the screenshot. As a result, I have to wait a long time for the tasks to finish again.
I have already used the -resume parameter. Why are the tasks being re-run? I look forward to your reply. Thank you very much.

linda
20251030

Command used and terminal output

Relevant files

No response

System information

No response

[lihuacao007]

Dear Developer,

Hello. I encountered the following issue when using nf-core/sarek to analyze my WES data (human, tumor and paired normal samples):

I first processed a batch of samples. After the tasks completed successfully, I added some new samples by modifying the samplesheet.csv file. However, when I ran the pipeline again, I found that the analyses for the first batch of already-completed samples were still being re-executed (e.g., BWA MEM), as shown in the screenshot. As a result, I have to wait a long time for the tasks to finish again.
I have already used the -resume parameter. Why are the tasks being re-run? I look forward to your reply. Thank you very much.

linda
20251104

[FriederikeHanssen]

Lookslike the attachements didn't get uploaded. It would in addition be helpful if you could provide us with the nextflow.log, the samplesheets and the terminal outputs

[lihuacao007]

Lookslike the attachements didn't get uploaded. It would in addition be helpful if you could provide us with the nextflow.log, the samplesheets and the terminal outputs

Apologies for the failed screenshot upload last time. As shown in the attachment (e.g., FASTQC), although this step had already been completed in the prior analysis, resubmitting the task—with modifications to the --tools parameter and the addition of new samples via updates to the samplesheet.csv file—triggered a re-run of FASTQC. The same behavior was observed for other tools, such as the time-consuming BWA-MEM.

[FriederikeHanssen]

Could you please attach the terminal outputs, the modified samplesheets, and the nextflow logs,? If you new samples are added to the samplesheet we would expect them to run through FastQC. are you observing that everything is rerun?