Merge pull request #88 from CCBR/feature/spook

Feature/spook

.github/workflows/test_dev.yml

@@ -7,7 +7,7 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: docker://snakemake/snakemake:v7.19.1
+    - uses: snakemake/snakemake-github-action@v1
       with:
         directory: '.test'
         snakefile: 'workflow/Snakefile'

config/config.yaml

@@ -74,7 +74,7 @@ macs2_control: "N"
 ## thresholds to be used for peak callers
 ## must be a list of comma separated values. minimum of numeric value required.
 ### default MACS2 qvalue is 0.05 https://manpages.ubuntu.com/manpages/xenial/man1/macs2_callpeak.1.html
-### default GOPEAKS pvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md
+### default GOPEAKS qvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md; [link to issue]
 ### default SEACR FDR threshold 1 https://github.com/FredHutch/SEACR/blob/master/README.md
 quality_thresholds: "0.1, 0.05"
 

workflow/Snakefile

@@ -223,8 +223,10 @@ rule all:
         # unpack(get_enrichment)
 
 # create jobby tables
-jobby_cmd = join(SCRIPTSDIR, 'resources', '_run_jobby_on_snakemake_log') + " " + join('logfiles', 'snakemake.log') + " | tee " + join('logfiles', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logfiles', 'snakemake.log.jobby.short')
-spook_cmd = join(SCRIPTSDIR, 'resources', '_spooker') + " " + WORKDIR + " | tee " + join('logfiles', 'spooker.log')
+## command for jobby: bash scripts/_run_jobby_on_snakemake_log logs/snakemake.log _jobby.py | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short
+## command for spooker: bash scripts/_spooker /data/sevillas2/carlisle/spook1 | tee logs/spooker.log
+jobby_cmd = "bash " + join(SCRIPTSDIR, '_run_jobby_on_snakemake_log') + " " + join('logs', 'snakemake.log') + " " + join(SCRIPTSDIR, '_jobby.py') + " | tee " + join('logs', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logs', 'snakemake.log.jobby.short')
+spook_cmd = "bash " + join(SCRIPTSDIR, '_spooker') + " " + WORKDIR + " | tee " + join('logs', 'spooker.log')
 
 onsuccess:
     print("OnSuccess")