nextflow docker container does not have conda inside

[inutano]

what?

then I had to create this one
https://github.com/inutano/docker-nextflow-with-conda

perhaps we can replace the current one in run.sh

[inutano]

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}