Looper/pipestat/issue update#102
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Fix smoothWig bugs. See #100
…more testing to follow
…precated now anyways so only will come up if we return it to usage
… pipeline intentionally to ensure proper handling of protocol
…tivate environment. still need to manually edit the sample_pipeline_interface.yaml conda_env value.
…eat is that it would apply to entire project run, not sample by sample. can add that at later date.
…ple specifications; close #38
…wig / _smooth.wig) via shell redirection rather than piping
Add tests/bulker_manifest.yaml with all PEPPRO tools including previously missing seqkit, seqtk, fastp, fastq_pair, and fqdedup. Bump bulker_crate version from 1.0.11 to 1.0.12 in both pipeline interface files. Add test-integration.sh runner script.
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Update PEPPRO to be compatible with changes to
looperandpipestatwhile addressing outstanding issues.