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Merge pull request #262 from vib-singlecell-nf/develop
Develop for v0.22.0 Former-commit-id: bf6f7c4
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,31 +1,32 @@ | ||
| process.afterScript = { | ||
| // Source: https://github.com/nextflow-io/nextflow/issues/1166#issuecomment-502467562 | ||
| process { | ||
| afterScript = { | ||
| // Source: https://github.com/nextflow-io/nextflow/issues/1166#issuecomment-502467562 | ||
| logMainDir = params.logDir | ||
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| logMainDir = params.logDir | ||
| // Check whether log dir is located in S3 if using awsbatch and is a local directory otherwise | ||
| if (workflow.profile == "aws") { | ||
| if (!logMainDir.matches("^s3://.*")) logMainDir = "s3:/" + workflow.workDir.toString() + "/log" | ||
| } else { | ||
| logMainDir = workflow.launchDir.resolve(logMainDir).toString() | ||
| if (!logMainDir.matches("^/.*")) logMainDir = workflow.launchDir.toString() + "/log" | ||
| } | ||
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| // Check whether log dir is located in S3 if using awsbatch and is a local directory otherwise | ||
| if (workflow.profile == "aws") { | ||
| if (!logMainDir.matches("^s3://.*")) logMainDir = "s3:/" + workflow.workDir.toString() + "/log" | ||
| } else { | ||
| logMainDir = workflow.launchDir.resolve(logMainDir).toString() | ||
| if (!logMainDir.matches("^/.*")) logMainDir = workflow.launchDir.toString() + "/log" | ||
| } | ||
| // Build log directory path based on task name | ||
| logSubDir = task.name.replace(" (null)", "").replace(" ", "/").replaceAll(" ", "_").replaceAll("[()]", "") | ||
| logDir = logMainDir + "/" + logSubDir | ||
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| // Build log directory path based on task name | ||
| logSubDir = task.name.replace(" (null)", "").replace(" ", "/").replaceAll(" ", "_").replaceAll("[()]", "") | ||
| logDir = logMainDir + "/" + logSubDir | ||
| // Define command to copy log files | ||
| cpLogCmd = workflow.profile == "aws" ? | ||
| "nxf_s3_upload '*.txt' ${logDir}; " : | ||
| "mkdir -p ${logDir}; cp -a *.txt ${logDir}; " | ||
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| // Define command to copy log files | ||
| cpLogCmd = workflow.profile == "aws" ? | ||
| "nxf_s3_upload '*.txt' ${logDir}; " : | ||
| "mkdir -p ${logDir}; cp -a *.txt ${logDir}; " | ||
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| // Assemble final command | ||
| cmd = "ls -alR --full-time > .command.ls; " | ||
| cmd += "mkdir nxf_log; " | ||
| cmd += "for file in .command.*; do cp -a \${file} nxf_log/\${file#.}.txt; done; " | ||
| cmd += "cd nxf_log; " | ||
| cmd += cpLogCmd | ||
| cmd += "cd ..;" | ||
| cmd | ||
| // Assemble final command | ||
| cmd = "ls -alR --full-time > .command.ls; " | ||
| cmd += "mkdir nxf_log; " | ||
| cmd += "for file in .command.*; do cp -a \${file} nxf_log/\${file#.}.txt; done; " | ||
| cmd += "cd nxf_log; " | ||
| cmd += cpLogCmd | ||
| cmd += "cd ..;" | ||
| cmd | ||
| } | ||
| } |
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