ci: debug dryrun on github actions

CCBR · Oct 16, 2023 · 7d1d251 · 7d1d251
1 parent e8a8db8
commit 7d1d251
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/.github/workflows/test_dev.yml b/.github/workflows/test_dev.yml
@@ -18,13 +18,15 @@ jobs:
         directory: '.test'
     - name: dryrun
       run: |
-        bash install.sh carlisle-dev
-        which carlisle
+        echo $PWD
+        bash ./install.sh carlisle-dev
         cd .test
         mkdir annotation
         for f in hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa
         do
           touch annotation/$f
         done
+        which carlisle
+        carlisle --runmode=init --workdir=./
         docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
-          snakemake --dryrun --configfile config_lint.yaml
+          carlisle --runmode=dryrun --workdir=./ --configfile config_lint.yaml