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lcdb / lcdb-wf

Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis
https://lcdb.github.io/lcdb-wf
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ChIP-seq pipeline requires all algorithms in config.yaml #166

Closed palmercd closed 5 years ago

palmercd commented 5 years ago

Due presumably to the recent fix for patterns population, the ChIP-seq pipeline now silently requires all supported algorithms (macs2, spp, sicer) to have at least one peak calling block in workflows/chipseq/config/config.yaml. Without this condition satisfied, the pipeline crashes with the error WildcardError in line 73 of /spin1/users/Lei/chipseq/chipseq-requires-callers/lcdb-wf/workflows/chipseq/Snakefile.test: Wildcards in input files cannot be determined from output files: 'sicer_run'

(or spp_run, etc)

Steps to reproduce: 1) install pipeline 2) generate an environment and activate it 3) in workflows/chipseq/config/config.yaml, delete all blocks from any one algorithm (sicer is easiest as there's only one example block) 4) in workflows/chipseq run bash ./run_test.sh

palmercd commented 5 years ago

For anyone seeing this before an actual clean fix happens, the following fixes the error (from top level lcdb-wf directory):

sed -i 's/if not d\[k\]:/if not d[k] and v.find("{") == -1 and v.find("}") == -1:/' lib/helpers.py