Comments (1)
testing it locally, can make a PR
git diff
diff --git a/sapporo/run.sh b/sapporo/run.sh
index ba75396..54caabc 100644
--- a/sapporo/run.sh
+++ b/sapporo/run.sh
@@ -31,7 +31,7 @@ function run_cwltool() {
}
function run_nextflow() {
- local container="nextflow/nextflow:22.04.4"
+ local container="ghcr.io/inutano/nextflow-with-conda:e2f9ff6"
local cmd_txt="docker run --rm ${D_SOCK} -v ${run_dir}:${run_dir} -w=${exe_dir} ${container} nextflow -dockerize run ${wf_url} ${wf_engine_params} -params-file ${wf_params} --outdir ${outputs_dir} -work-dir ${exe_dir} 1>${stdout} 2>${stderr}"
find ${exe_dir} -type f -exec chmod 777 {} \;
echo ${cmd_txt} >${cmd}
from sapporo-service.
Related Issues (15)
- SAPPORO-service's Logger Bug
- Public sapporo-service server HOT 1
- Nextflow core/GitHub-URL runner HOT 3
- Singularity support
- Doesn't display service add error
- Clean up the contents of `run_dir` HOT 2
- sapporo CLI cannot correctly find --run-sh path given relative path from current dir HOT 2
- Automatically discover the workflow engine versions? HOT 3
- Use Nextflow
- The issue when accessing API (/service-info) HOT 6
- WES 1.1.0 `worfklow_engine` HOT 2
- 2.0.1 installation fails HOT 1
- Use WDL
- Modify API-definision
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