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Added trimming step using trimGalore and logging. 1 of 7 checklist items completed
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Resolve "Add CI for Trim" 0 of 7 checklist items completed
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Resolve "process_createManifest" 3 of 3 checklist items completed
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Resolve "process_align" 0 of 4 checklist items completed
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Resolve "process_getRef" 3 of 3 checklist items completed
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Resolve "process_fastqc" 3 of 3 checklist items completed
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Resolve "process_makeBigWig" 3 of 3 checklist items completed
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Resolve "Update design docs" 5 of 5 checklist items completed
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Resolve "process_count" 4 of 4 checklist items completed
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Resolve "process_RSeQC" 4 of 4 checklist items completed
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Resolve "Move inference to start of pipeline" 5 of 6 checklist items completed
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Resolve "process_qc" 6 of 8 checklist items completed
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Resolve "Add input bagit to ouput" 4 of 10 checklist items completed
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Test failure. 5 of 10 checklist items completed
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Resolve "Output tool version to report in multiqc" 7 of 12 checklist items completed
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WIP: Resolve "Change yes/no metadata to bool" 3 of 12 checklist items completed
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