Fix tools writing to Galaxy's files directory #3991
Description
With galaxyproject/planemo#1190 its possible to detect tools that write to Galaxy's files directory. I'm running this on IUC here: https://github.com/bernt-matthias/tools-iuc/runs/3721212988?check_suite_focus=true
See also discussion in #3986 (comment)
Here is a list of tools (from an earlier run of the CI workflow) that create at least one extra file:
- emboss .dat.1.png
- bacteria_tradis .dat.bwt ...
- barrnap .dat.fai barrnap avoid writing to inputdir #4104
- commet .dat_multi_k31_s4.h5
- crossmap_* .dat.fai .unmap Symlink crossmap_vcf fasta input to prevent writing to the input directory to generate fasta index #4126
- delly_* .dat.fai
- discosnp_pp .dat_multi_k31_s4.h5
- fermikit fermikit: avoid writing to inputdir #4105
- fermi2 .dat.fai
- fermikit_variants .dat.fai
- hyphy_* .dat.fit.bf
- irissv .dat.bai Irissv: fix errors related to bai file creation #4642
1.0.4+galaxy2 - kissplice .dat_multi_k31_s4.h5
- lordec .dat_multi_k31_s4.h5
- mapsembler2 .dat_multi_k31_s4.h5
- medaka_* .dat.fai ...
- nanocompore_* .dat.fai
- picard_* .dat.bai
- progressivemauve .dat.backbone
- pyega3 .dat.md5
- stringtie* .dat.bak
- takeabreak .dat_multi_k31_s4.h5
- tetyper .dat.nto ... tetyper: avoid writing indices to inputdir #4107
- tradis_* .dat.bwt .. Bio-TraDis: avoid writing to input directory #4103
- xmfa2gff3 .dat.backbone
I hope that the PR is accepted soon. Then it will also run for PRs.
Put your name / PR number next to the entries if you are working on one of the tools above.