Nextflow issues

[iddryg]

Hi, I just tried to process my .scn files using the nextflow method.

First issue: the documentation says to run "nextflow run adamjtaylor/scn2ometiff ....." which didn't work. I was able to fix this by updating the git repo from adamjtaylor to ncihtan and it ran successfully: "nextflow run ncihtan/scn2ometiff .........". You could update your readme and should be all good there.

When I ran it, I encountered some errors. Haven't been able to think too critically about these but here they are...

(SRRS2022) [iddryg@crux 2023_02_SCN_conversion]$ ~/nextflow run ncihtan/scn2ometiff -r nf --input ./scn_files/*.scn --output output
N E X T F L O W  ~  version 22.10.6
Pulling ncihtan/scn2ometiff ...
 downloaded from https://github.com/ncihtan/scn2ometiff.git
Launching `https://github.com/ncihtan/scn2ometiff` [friendly_yonath] DSL2 - revision: c82477c4a4 [nf]
executor >  local (1)
[8d/235928] process > count_scenes (1) [  0%] 0 of 1
[-        ] process > bioformats2raw   -
[-        ] process > clean_ome        -
[-        ] process > raw2ometiff      -
Error executing process > 'count_scenes (1)'

Caused by:
  Process `count_scenes (1)` terminated with an error exit status (126)

Command executed:

  tiffcomment FILENAME1.scn| grep -c '</image>'

executor >  local (1)
[8d/235928] process > count_scenes (1) [100%] 1 of 1, failed: 1 ✘
[-        ] process > bioformats2raw   -
[-        ] process > clean_ome        -
[-        ] process > raw2ometiff      -
Error executing process > 'count_scenes (1)'

Caused by:
  Process `count_scenes (1)` terminated with an error exit status (126)

Command executed:

  tiffcomment FILENAME1.scn| grep -c '</image>'

Command exit status:
  126

Command output:
  (empty)

Command error:
  docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-IGBiZFyyPDPc3JOy9d21Zwb6": dial unix /var/run/docker.sock: connect: permission denied.
  See 'docker run --help'.

Work dir:
  /immuno/ian/Projects/SRRS2022/2023_02_SCN_conversion/work/8d/235928eebbf86874c11d643258ab0a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

[adamjtaylor]

Thanks Ian... I'm still working on the Nextflow workflow, but in the meantime could you test using the docker container (see updated readme).

If you prefer ImageJ I think the Kehops plugin also does a good job at both splitting out scenes from the scn file and providing 'clean' OME-XML metadata. Would your report if you can use that successfully?

Thank you!

[iddryg]

Tried the docker container, got permission denied.

$ docker run -it --rm -v /homes1/iddryg/ian/Projects/SRRS2022/2023_02_SCN_conversion/scn_files adamjtaylor/scn2ometiff /bin/bash -c "/convert_scn.sh /data/.scn"

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create": dial unix /var/run/docker.sock: connect: permission denied.