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I've set cromwell (30.2) to only use hard-link and soft-link to localize files (so I removed "copy" from the available options). However, I keep getting these errors:
Could not localize /data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz -> /data/Experiment/redmar/Experiment_105/cromwell-executions/trim/cd1ba924-bd0d-4f75-af05-924555364a73/call-before/shard-34/inputs/data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz: /data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz doesn't exists /data/Experiment/redmar/Experiment_105/cromwell-executions/trim/cd1ba924-bd0d-4f75-af05-924555364a73/call-before/shard-34/inputs/data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz -> /data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz: Operation not permitted
I've tried manually linking the required files into the cromwell folder using
ln -s, which works.
I'm not the owner of the /data/reads/illumina/nvwa/103200-007/rawdata/103200-007-035_2.fastq.gz file, and I'm using docker, so I'm not sure if that has something to do with this issue.
The weird thing is that the workflow doesn't terminate due to this errors, it just goes to the next shard or the next task, and keeps creating
execution folders, without placing anything in them. It also creates the
inputs folder and the hierarchy inside it, but then it doesn't actually localize any of the files.