Reached automation hook - Nextflow doesnt move on

apeltzer · September 16, 2024, 7:36am

Hi everyone! I have a few pipeline runs that I’ve been running successfully (demultiplex, smrnaseq, rnaseq) and all of them finished successfully. Unfortunately, the pipeline finished and then stalled just showing this warning/error:

“Reached automation hook …”

After which, nothing happens. My suspicion is that the --hook_url doesnt work, if I test it manually though its successfully working. Anyone have seen this previously?

apeltzer · September 16, 2024, 8:06am

Also a bit weird, once I cancel this, the email gets sent and the webhook is also sent properly - but the overall status then changes to cancelled (all data was there already / all copied fine).

kenibrewer · September 22, 2024, 5:14pm

Hi Alexander,
I haven’t done much with the “hook-url” before, but given that I don’t see “Reached automation hook” anywhere in the nf-core/rnaseq codebase, I think this might be line that where it’s being generated:

github.com

nf-core/rnaseq/blob/4053b2ec173fc0cfdd13ff2b51cfaceb59f783cb/subworkflows/nf-core/utils_nfcore_pipeline/main.nf#L443


      
              def json_message  = json_template.toString()
          
              // POST
              def post = new URL(hook_url).openConnection();
              post.setRequestMethod("POST")
              post.setDoOutput(true)
              post.setRequestProperty("Content-Type", "application/json")
              post.getOutputStream().write(json_message.getBytes("UTF-8"));
              def postRC = post.getResponseCode();
              if (! postRC.equals(200)) {
                  log.warn(post.getErrorStream().getText());
              }
          }

Maybe to troubleshoot you could try adding some code to that function to dump hook_url and the json_message before the post?

apeltzer · September 24, 2024, 2:48pm

Good one, I’ll try that. Once I remove hook_url and email, it just works without issue at all.

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Reached automation hook - Nextflow doesnt move on

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