Module stub that `touch .gz` break snapshots in `nf-test`

[awgymer]

Have you checked the docs?

• [X] nf-core website: troubleshooting
• [X] nf-core modules documentation

Description of the bug

Per this slack thread it seems that empty .gz files generated by simply touch <filename>.gz break the snapshot functionality of nf-test by causing an EOFException because the files are not actually compressed.

Per this comment a fix is to replace the touch command with echo "" | gzip > <filename>.gz.

A git grep -cP "touch .*\.gz(\s+.*)*$" identifies the following 71 modules as using this pattern:

• [ ] arriba/download
• [ ] art/illumina
• [ ] bcftools/call
• [ ] bcftools/concat
• [ ] bedgovcf
• [ ] bowtie2/align
• [ ] cadd
• [ ] cat/fastq
• [ ] cellrangerarc/mkfastq
• [ ] cellrangeratac/mkfastq
• [ ] deepvariant
• [ ] delly/call
• [ ] ensemblvep/vep
• [ ] expansionhunter
• [ ] fcs/fcsadaptor
• [ ] gatk4/applyvqsr
• [ ] gatk4/filtermutectcalls
• [ ] gatk4/genotypegvcfs
• [ ] gatk4/haplotypecaller
• [ ] gatk4/mergevcfs
• [ ] gatk4/mutect2
• [ ] gatk4/postprocessgermlinecnvcalls
• [ ] gatk4/reblockgvcf
• [ ] gatk4/samtofastq
• [ ] gatk4/selectvariants
• [ ] gatk4/variantfiltration
• [ ] genomad/endtoend
• [ ] getorganelle/fromreads
• [ ] gfastats
• [ ] gfatools/gfa2fa
• [ ] glimpse/concordance
• [ ] glimpse2/concordance
• [ ] happy/happy
• [ ] icountmini/peaks
• [ ] icountmini/sigxls
• [ ] jasminesv
• [ ] kmcp/search
• [ ] lofreq/somatic
• [x] mosdepth
• [ ] nanofilt
• [ ] ngmerge
• [ ] parabricks/mutectcaller
• [ ] paragraph/multigrmpy
• [ ] paragraph/vcf2paragraph
• [ ] pharokka/installdatabases
• [ ] picard/liftovervcf
• [ ] picard/renamesampleinvcf
• [ ] picard/sortvcf
• [ ] popscle/dscpileup
• [ ] prodigal
• [ ] pyrodigal
• [ ] rtgtools/vcfeval
• [ ] sentieon/applyvarcal
• [ ] sentieon/dnamodelapply
• [ ] sentieon/dnascope
• [ ] sentieon/gvcftyper
• [ ] sentieon/haplotyper
• [ ] sentieon/tnfilter
• [ ] sentieon/tnhaplotyper2
• [ ] sentieon/tnscope
• [ ] seqkit/grep
• [ ] shapeit5/switch
• [ ] sortmerna
• [ ] star/align
• [ ] stranger
• [ ] svaba
• [ ] svanalyzer/svbenchmark
• [ ] svdb/merge
• [ ] truvari/bench
• [ ] vcflib/vcfbreakmulti
• [ ] vt/decompose
• [ ] vt/normalize

[famosab]

For wittyer the code in the stub test actually looks like this:

    touch ${prefix}.json
    echo "" | gzip > ${prefix}.vcf.gz
    touch ${prefix}.vcf.gz.tbi

When I tested the module using touch to create the .gz.tbi file did not lead to errors when asserting { assert snapshot(process.out).match() }, so it seems to me that you would only need to search for modules where the file extension ends with .gz.

[awgymer]

The list was generated before I had tested .gz.* type files. It does indeed seem that these are not an issue for nf-test (I think it does a naive check for .gz file extension before it tries opening as a gzipped file?).

I've revised the list with a regex that excludes such files.