[FEATURE] nf-test assertions - use md5 sums for readLines
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nf-test
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Description
Is your feature request related to a problem? Please describe
Sometimes parts of output files have timestamps or similar stuff in them which makes the total md5sum of the file itself instable. Thus we usally go for asserting the lines with readLines() or even just the name.
Describe the solution you'd like
I suggest using
file.readLines()[2..-1].join('\n').md5()
to create md5sums for the stable parts. This makes the snapshots smaller :)
List of modules / sbwfs this can be applied to
Some of them might also benefit from nf-test plugins
- hicap
- toulligqc
- plasmidfinder
- bam_qc_picard
- sistr
- optitype
- fastme
- fastq_qc_trim_filter_setstrandedness
- paraphase
- bandage/image
- interproscan
- umitools/group
- motus/profile
- picard/markduplicates
- bbmap/sendsketch
- integronfinder
- geoquery/getgeo
- bcftools/stats
- vcf2maf
- seqsero2
- issero
- metaphlan/metaphlan
- purecn/intervalfile
- gappa/examineheattree
- methyldackel/mbias
- entrezdirect/esummary
- muse/call
- bowtie2/align
- snippy/run
- porechop/abi
- controllfreec/freec2bed
- nucmer
- gstama/collapse
- homer_groseq
- scimap/mcmicro
- picard/collecthsmetrics
- qcat
- mapdamage2
- biobambam/bammarkduplicates2
- kallistobustools/count
- controlfreec/freec
- fcsgx/rungx
- picard/collectinsertsizemetrics
- cafe
- gatk4/mergemutectstats
- iqtree
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the nf-test assertion and snapshot handling for readLines() and md5 values. Use the requested stable-line hash behavior as the completion criterion, then review the listed modules for applicable snapshot updates.
Written by the indexing model from the issue text.
Assessment
- Domain
- testing-qa
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100