Fix tests after modules repository restructuring

[JoseEspinosa]

After https://github.com/nf-core/modules/pull/2141 was merged tests failed in the following modules as nicely reported by @grst in modules slack Please assign yourself by editing this issue e.g. - [ ] module/foo (@JoseEspinosa) and mark it as resolved when your PR fixing the test is merged.

• [x] amps #3244
• [x] amrfinderplus/run @rpetit3
• [x] amrfinderplus/update @rpetit3
• [x] antismash/antismashlitel (not failing, cf #2687 and #2688 )
• [x] antismash/antismashlitedownloaddatabasesl (not failing, cf #2687 and #2688 )
• [x] arriba (@JoseEspinosa)
• [x] bamcmp #3245
• [X] bases2fastq (@Emiller88 https://github.com/nf-core/modules/pull/2074)
• [x] bcftools/reheader #2497
• [x] bcftools/sort #2497
• [x] biscuit/epiread #2475
• [x] checkm/qa (not failing, cf #2464)
• [x] cnvkit/batch #2492
• [x] controlfreec/assesssignificance #3248
• [x] controlfreec/freec #2980
• [x] controlfreec/freec2bed #3248
• [x] controlfreec/freec2circos #3248
• [x] controlfreec/makegraph #3248
• [x] cooler/cload @pawelciurkaardigen (https://github.com/nf-core/modules/pull/2219)
• [x] cooler/zoomify #1937
• [x] custom/sratoolsncbisettings #3964
• [ ] deeparg/downloaddata tracked in #4321
• [ ] deeparg/predict tracked in #4321
• [x] deepvariant #2494
• [x] delly/call #2909 and #3246
• [x] endorspy #3134
• [x] entrezdirect/esearch #3243
• [x] ffq #3978
• [x] flye #3977
• [x] freebayes #2493 #3242
• [x] gatk4/applybqsr @pawelciurkaardigen (https://github.com/nf-core/modules/pull/2219)
• [x] gatk4/genotypegvcfs @pawelciurkaardigen
• [x] gatk4/mutect2 @pawelciurkaardigen
• [x] gtdbtk/classifywf #16665
• [x] kallistobustools/ref (not failing)
• [x] leehom @chriswyatt1 (need PR review)
• [x] mafft (Seems to work fine- @chriswyatt1, confirmed by @muffato )
• [x] maltextract @chriswyatt1 (need PR review)
• [x] maxquant/lfq (not failing)
• [x] metaphlan3/mergemetaphlantables #3976
• [x] motus/downloaddb #2631
• [x] motus/merge #2631 (Conda failure dismissed https://github.com/nf-core/modules/pull/2631#issuecomment-1345626513 )
• [x] motus/profile #2631 (Conda failure dismissed https://github.com/nf-core/modules/pull/2631#issuecomment-1345626513 )
• [x] nanoplot #2610
• [x] ncbigenomedownload @chriswyatt1
• [x] pairtools/dedup #3247
• [x] pairtools/flip #3247
• [x] pairtools/restrict #3247
• [x] picard/sortvcf @pawelciurkaardigen
• [x] pirate @rpetit3
• [x] plasmidid #3746
• [ ] plink2/extract - tracked in #3965
• [x] rtgtools/vcfeval (not failing, cf #2734)
• [x] shovill @rpetit3
• [x] sistr @rpetit3
• [x] stranger @pawelciurkaardigen (singularity and docker pass, for conda there is a problem creating conda environment - PackagesNotFound)
• [x] strelka/somatic (not failing)
• [x] tbprofiler/profile @rpetit3
• [x] ultra/pipeline #2479
• [ ] unicycler - tracked in #3982
• [x] yara/mapper (#2164)
• [x] ariba/run @rpetit3
• [x] busco @rpetit3
• [x] dragonflye @rpetit3
• [x] mobsuite/recon @rpetit3
• [x] panaroo/run @rpetit3
• [x] prokka @rpetit3
• [x] roary @rpetit3
• [x] snippy/core @rpetit3
• [x] snippy/run @rpetit3

[rpetit3]

No Fixes needed (Tests (TMPDIR=~ nf-core modules test) passed with conda, docker, singularty)

• ariba/run
• busco
• dragonflye
• mobsuite/recon
• panaroo/run
• prokka
• roary
• sistr
• snippy/core
• snippy/run
• gatk4/genotypegvcfs
• gatk4/mutect2

[amasplund]

We have looked at bcftools/sort and it looks like the md5sum of the zipped output vcf-file is different if you use a conda or docker profile. If you unzip the files the md5sum is the same. The docker one is the same as what is stated in the tests/modules/nf-core/bcftools/sort/test.yml file. Seems like a problem that should probably have appeared before!? Is there a standard solution? Remove the md5sum check of the zipped file??

[pawelciurkaardigen]

@amasplund I had similar problem for gatk4/applybqsr and validating cram file's md5sum but for me it was depending if I run the test locally or in CI. My solution was, as you suggested, relaxing the assertion by removing md5sum which is validating only file's presence. I don't know however if there is a better way that preserves file's content verification.

[muffato]

I found quite a few that have been fixed in the past few weeks

[muffato]

(I've assigned this ticket to myself because I'll try to go through those issues one by one, but please don't hold me responsible for everything 😅 !)

[muffato]

Finally getting to the bottom of this !

1. I've forked two issues for broken tests: #3965 and #3982
2. The deeparg/downloaddata test is failing because the underlying deeparg version, 1.0.2, needs data from a website that is gone. There is no command-line parameter to change the URL and there is no other version. I've sent an email to the author about it.
3. The deeparg/predict test fails because it first runs deeparg/downloaddata

My goal is to close this ticket once I've got an answer from the deeparg author.

[muffato]

Deeparg issue tracked in #4321