add NXF_SCRATCH=$LSF_TMPDIR to nextflow configs on LSF cluster#90
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jbrestel wants to merge 1 commit into
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add NXF_SCRATCH=$LSF_TMPDIR to nextflow configs on LSF cluster#90jbrestel wants to merge 1 commit into
jbrestel wants to merge 1 commit into
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…F cluster
All Make*NextflowConfig workflow steps now include env { NXF_SCRATCH = '$LSF_TMPDIR' }
in the generated nextflow.config when the cluster executor is LSF. OrthoFinder configs
(which already had an env block) have the variable inserted inline rather than as a
separate block.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
getNextflowLsfScratchEnvBlock()helper toWorkflowStep.pmthat returnsenv { NXF_SCRATCH = '$LSF_TMPDIR' }when the executor is LSF, empty string otherwiseMake*NextflowConfigworkflow steps to include this block in the generatednextflow.configwhen running on LSFenv {}block with JVM settings) haveNXF_SCRATCHinserted inline into the existing block rather than as a separate blockMakeLoadCNVNextflowConfig,MakeDnaSeqMergeExperimentsNextflowConfig,MakeStudyAssayResultsNextflowConfig,MakeRnaSeqAnalysisNextflowConfig) are unchangedTest plan
nextflow.configcontainsNXF_SCRATCH = '$LSF_TMPDIR'NXF_SCRATCHNXF_SCRATCHinside the singleenv {}block alongside the JVM settings🤖 Generated with Claude Code