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lskatz / SneakerNet

:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Apache License 2.0
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bcl2fastq missed #30

Closed kapsakcj closed 4 years ago

kapsakcj commented 4 years ago

Describe the bug bcl2fastq isn't checked for in checkdeps.pl scripts, or listed in the install.md docs

I also did not put it in the Dockerfile

To Reproduce Steps to reproduce the behavior:

docker run --rm -v $PWD:/data -u $(id -u):$(id -g) lskatz/sneakernet:latest SneakerNet.roRun.pl /data/$MISEQ -o /data/$INDIR
SneakerNet.roRun.pl: ERROR: no interop files were found in /data/miseq-rundir/
SneakerNet.roRun.pl: snok.txt not found. I will not read from it.
SneakerNet.roRun.pl: WARNING: no fastq files were found; attempting bcl2fastq
sh: 1: bcl2fastq: not found

Expected behavior bcl2fastq needs to be listed in docs

It also needs to be added to the dockerfile and added to the PATH as specified in dockerfile

kapsakcj commented 4 years ago

I will do a PR to add bcl2fastq to the Dockerfile

lskatz commented 4 years ago

Added PR from @kapsakcj in 29fff06e5141d19b3680e954b822da53a6aada98 and added documentation in 09d4821e703249d56f36a3d4d53de6d22ad33afb