Hello,
when I run the command : dockstore tool launch --entry --script quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json.txt
This downloads all the files in the github repository to the datastore directory, but doesn't run the alignment pipeline afterwards, citing that the bam.bai's are not present in a merging step.
ERROR [job Seqware-BWA-Workflow] Job error:
("Error collecting output for parameter 'merged_output_bai': ../../../tmp/1691622356648-0/Dockstore.cwl:94:7: Did not find output file with glob pattern: '['datastore/hg19.chr22.5x.normal.bam.bai']'.", {})
There's no bam.bai's present in the current repository. I'm not sure if the pipeline is supposed to generate this. Plase let me know if you can assist with this.
dockstore_launch.log
Best,
-Ashraf
Hello,
when I run the command : dockstore tool launch --entry --script quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json.txt
This downloads all the files in the github repository to the datastore directory, but doesn't run the alignment pipeline afterwards, citing that the bam.bai's are not present in a merging step.
ERROR [job Seqware-BWA-Workflow] Job error:
("Error collecting output for parameter 'merged_output_bai': ../../../tmp/1691622356648-0/Dockstore.cwl:94:7: Did not find output file with glob pattern: '['datastore/hg19.chr22.5x.normal.bam.bai']'.", {})
There's no bam.bai's present in the current repository. I'm not sure if the pipeline is supposed to generate this. Plase let me know if you can assist with this.
dockstore_launch.log
Best,
-Ashraf