Fix failing tests after data restructuring

[KevinMenden]

This is a list of all module tests that we need to get the tests passing for again: Please assign yourself by editing this issue:

• [x] bowtie2/align (assigned @JoseEspinosa )
• [x] bowtie2/build_test (assigned @JoseEspinosa )
• [x] bwameth/align (assigned @JoseEspinosa )
• [x] bwameth/index (assigned @JoseEspinosa )
• [x] multiqc (assigned @JoseEspinosa )
• [x] gffread (assigned @KevinMenden )
• [x] sequenzautils/gcwiggle (assigned @KevinMenden )
• [x] homer/annotatepeaks (assigned @KevinMenden )
• [ ] bandage/image (assigned @KevinMenden )
• [x] seqwish/induce (assigned @KevinMenden )
• [x] salmon/index (assigned to @BatoolMM )
• [x] salmon/quant (assigned to @BatoolMM)
• [x] trimgalore (@grst)
• [x] picard/markduplicates (@grst)
• [x] picard/mergesamfiles (@grst)
• [x] picard/collectmultiplemetrics (@grst)
• [x] picard/collectwgsmetrics (@grst)
• [x] minia
• [x] pangolin (@rpetit3)
• [x] minimap2/align (@yuukiiwa)
• [x] vcftools (@KevinMenden )
• [x] bismark/report (@KevinMenden )
• [x] bismark/align (@KevinMenden )
• [x] bismark/genomepreparation (@KevinMenden )
• [x] bismark/summary (@KevinMenden )
• [x] bismark/deduplicate (@KevinMenden )
• [x] bismark/methylationextractor (@KevinMenden )
• [x] untar (@JoseEspinosa )
• [x] cat/fastq (@JoseEspinosa )
• [x] blast/blastn (@rpetit3)
• [x] blast/makeblastdb (@rpetit3)
• [x] kraken2/run (@JoseEspinosa )
• [x] bedtools/genomecov (✔️ @drpatelh)
• [x] bedtools/slop (✔️ @drpatelh)
• [x] bedtools/merge (✔️ @drpatelh)
• [x] bedtools/getfasta (✔️ @drpatelh)
• [x] bedtools/sort (✔️ @drpatelh)
• [x] bedtools/complement (✔️ @drpatelh)
• [x] bedtools/intersect (✔️ @drpatelh)
• [x] bedtools/maskfasta (✔️ @drpatelh)
• [x] gunzip (@fullama)
• [x] preseq/lcextrap (@rpetit3)
• [x] spades (@rpetit3)
• [x] bwa/mem @FriederikeHanssen
• [x] bwa/index @FriederikeHanssen
• [ ] unicycler (@rpetit3)
• [x] bwamem2/mem @FriederikeHanssen
• [x] bwamem2/index @FriederikeHanssen
• [x] bcftools/stats (assigned @Mark-S-Hill)
• [x] bcftools/isec (assigned @Mark-S-Hill)
• [x] bcftools/filter (assigned @Mark-S-Hill)
• [x] bcftools/consensus (assigned @Mark-S-Hill)
• [x] bcftools/mpileup (assigned @Mark-S-Hill)
• [x] bcftools/merge (assigned @Mark-S-Hill)
• [ ] star/align (@rpetit3)
• [ ] star/genomegenerate (@rpetit3)
• [X] tabix/tabix (@rpetit3)
• [X] tabix/bgzip (@rpetit3)
• [x] optitype (@rpetit3)
• [x] samtools/view(assigned @arontommi )
• [x] samtools/stats(assigned @arontommi )
• [x] samtools/flagstat(assigned @arontommi )
• [x] samtools/faidx(assigned @arontommi )
• [x] samtools/mpileup(assigned @arontommi )
• [x] samtools/index(assigned @arontommi )
• [x] samtools/fastq(assigned @arontommi )
• [x] samtools/merge(assigned @arontommi )
• [x] samtools/sort(assigned @arontommi )
• [x] samtools/idxstats(assigned @arontommi )
• [x] stringtie (@yuukiiwa)
• [x] bowtie/align (@yuukiiwa)
• [x] bowtie/build_test (@yuukiiwa)
• [x] seqkit/split2 @FriederikeHanssen
• [x] prokka (@fullama)
• [x] gatk4/createsequencedictionary (@suzannejin)
• [x] gatk4/variantfiltration (assigned @Mark-S-Hill)
• [x] gatk4/bedtointervallist (@suzannejin)
• [x] gatk4/samtofastq (@suzannejin)
• [x] gatk4/splitncigarreads (@suzannejin)
• [x] gatk4/fastqtosam (@suzannejin)
• [x] gatk4/revertsam (@suzannejin)
• [x] gatk4/mergebamalignment (@suzannejin)
• [x] gatk4/applybqsr (@suzannejin)
• [x] gatk4/baserecalibrator (@suzannejin)
• [x] gatk4/mergevcfs (@suzannejin)
• [ ] flash (@rpetit3)
• [x] mosdepth (@rpetit3)
• [ ] seacr/callpeak (@rpetit3)
• [x] prodigal (@fullama)
• [x] quast (@rpetit3)
• [x] cnvkit (@fullama)
• [x] ivar/consensus (@fullama)
• [x] ivar/variants (@fullama)
• [x] ivar/trim (@fullama)
• [x] fastp (✔️ @drpatelh)
• [x] allelecounter (@fullama)
• [x] cutadapt (@fullama)
• [x] fastqc (✔️ @drpatelh)
• [x] tiddit/sv (@rpetit3)
• [x] methyldackel/mbias (@rpetit3)
• [x] methyldackel/extract (@rpetit3)
• [x] qualimap/bamqc (@rpetit3)
• [x] ucsc/bed12tobigbed (@yuukiiwa)
• [x] ucsc/bedgraphtobigwig (@yuukiiwa)
• [ ] shovill (@rpetit3)
• [x] adapterremoval (@pericsson)
• [ ] strelka/germline @FriederikeHanssen
• [x] dsh/splitbed (@pericsson)
• [x] dsh/filterbed (@pericsson)

[drpatelh]

The disadvantage of closing an uber, super, large issue linked to a PR 😆

[KevinMenden]

I think we're pretty much done here, except for a few modules that don't have proper test data anyway :+1:

[grst]

Closed this in favor of https://github.com/nf-core/modules/issues/745.