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

[awgymer]

Have you checked the docs?

• nf-core website: troubleshooting
• 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
• 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.