Fix `versions.yml` in all modules

grst commented 3 years ago

COMPLETED

[x] abacas (assigned @drpatelh)
[x] agrvate (assigned @drpatelh)
[x] bandage/image (assigned @drpatelh)
[x] bismark/align (assigned @drpatelh)
[x] bismark/deduplicate (assigned @drpatelh)
[x] bismark/genomepreparation (assigned @drpatelh)
[x] bismark/methylationextractor (assigned @drpatelh)
[x] bismark/report (assigned @drpatelh)
[x] bismark/summary (assigned @drpatelh)
[x] bowtie/align (assigned @drpatelh)
[x] bowtie/build (assigned @drpatelh)
[x] bowtie2/align (assigned @drpatelh)
[x] bowtie2/build (assigned @drpatelh)
[x] bwa/aln (assigned @drpatelh)
[x] bwa/index (assigned @drpatelh)
[x] bwa/mem (assigned @drpatelh)
[x] bwa/sampe (assigned @drpatelh)
[x] bwa/samse (assigned @drpatelh)
[x] bwamem2/index (assigned @drpatelh)
[x] bwamem2/mem (assigned @drpatelh)
[x] bwameth/align (assigned @drpatelh)
[x] bwameth/index (assigned @drpatelh)
[x] cat/fastq (assigned @drpatelh)
[x] chromap/chromap (assigned @rpetit3)
[x] delly/call (assigned @rpetit3)
[x] ensemblvep (assigned @rpetit3)
[x] expansionhunter (assigned @rpetit3)
[x] fgbio/callmolecularconsensusreads (assigned @rpetit3)
[x] fgbio/sortbam (assigned @rpetit3)
[x] flash (assigned @drpatelh)
[x] gatk4/applybqsr (assigned @drpatelh)
[x] gatk4/baserecalibrator (assigned @drpatelh)
[x] gatk4/bedtointervallist (assigned @drpatelh)
[x] gatk4/createsequencedictionary (assigned @drpatelh)
[x] gatk4/fastqtosam (assigned @drpatelh)
[x] gatk4/getpileupsummaries (assigned @drpatelh)
[x] gatk4/haplotypecaller (assigned @drpatelh)
[x] gatk4/intervallisttools (assigned @drpatelh)
[x] gatk4/markduplicates (assigned @drpatelh)
[x] gatk4/mergebamalignment (assigned @drpatelh)
[x] gatk4/mergevcfs (assigned @drpatelh)
[x] gatk4/mutect2 (assigned @drpatelh)
[x] gatk4/revertsam (assigned @drpatelh)
[x] gatk4/samtofastq (assigned @drpatelh)
[x] gatk4/splitncigarreads (assigned @drpatelh)
[x] gatk4/variantfiltration (assigned @drpatelh)
[x] genmap/index (assigned @drpatelh)
[x] glnexus (assigned @rpetit3)
[x] graphmap2/align (assigned @drpatelh)
[x] graphmap2/index (assigned @drpatelh)
[x] gunzip (assigned @drpatelh)
[x] hifiasm (assigned @rpetit3)
[x] iqtree (assigned @jfy133)
[x] ivar/consensus (assigned @drpatelh)
[x] ivar/trim (assigned @drpatelh)
[x] ivar/variants (assigned @drpatelh)
[x] kallisto/index (assigned @JoseEspinosa)
[x] kallistobustools/count (assigned @JoseEspinosa)
[x] kallistobustools/ref (assigned @JoseEspinosa)
[x] kleborate (assigned @rpetit3)
[x] kraken2/kraken2 (assigned @drpatelh)
[x] lofreq/call (assigned @drpatelh)
[x] lofreq/callparallel (assigned @drpatelh)
[x] lofreq/filter (assigned @drpatelh)
[x] lofreq/indelqual (assigned @drpatelh)
[x] methyldackel/extract (assigned @drpatelh)
[x] methyldackel/mbias (assigned @drpatelh)
[x] minia (assigned @rpetit3)
[x] nanoplot (assigned @JoseEspinosa)
[x] optitype (assigned @JoseEspinosa, issue opened #783)
[x] pairix (assigned @JoseEspinosa)
[x] pbccs (assigned @JoseEspinosa)
[x] picard/markduplicates (assigned @jfy133)
[x] picard/mergesamfiles(assigned @jfy133)
[x] plasmidid (assigned @JoseEspinosa)
[x] plink/vcf (assigned @jfy133)
[x] preseq/lcextrap (assigned @drpatelh)
[x] prokka (assigned @JoseEspinosa)
[x] pydamage/analyze (assigned @jfy133)
[x] pydamage/filter (assigned @jfy133)
[x] qualimap/bamqc (assigned @drpatelh)
[x] raxmlng (assigned @JoseEspinosa)
[x] rsem/preparereference (assigned @drpatelh)
[x] salmon/index (assigned @drpatelh)
[x] samtools/ampliconclip (assigned @drpatelh)
[x] samtools/faidx (assigned @drpatelh)
[x] samtools/fastq (assigned @drpatelh)
[x] samtools/flagstat (assigned @drpatelh)
[x] samtools/idxstats (assigned @drpatelh)
[x] samtools/index (assigned @drpatelh)
[x] samtools/merge (assigned @drpatelh)
[x] samtools/mpileup (assigned @drpatelh)
[x] samtools/sort (assigned @drpatelh)
[x] samtools/stats (assigned @drpatelh)
[x] samtools/view (assigned @drpatelh)
[x] seacr/callpeak (assigned @drpatelh)
[x] seqkit/split2 (assigned @drpatelh)
[x] seqtk/sample (assigned @drpatelh)
[x] seqtk/subseq (assigned @drpatelh)
[x] sequenzautils/bam2seqz (assigned @drpatelh)
[x] sequenzautils/gcwiggle (assigned @drpatelh)
[x] shovill (assigned @JoseEspinosa)
[x] snpeff (assigned @jfy133)
[x] star/genomegenerate (assigned @drpatelh)
[x] stringtie/merge (assigned @drpatelh)
[x] stringtie/stringtie (assigned @drpatelh)
[x] subread/featurecounts (assigned @grst)
[x] tabix/bgzip (assigned @drpatelh)
[x] tabix/bgziptabix (assigned @drpatelh)
[x] tabix/tabix (assigned @drpatelh)
[x] tiddit/sv (assigned @drpatelh)
[x] trimgalore (assigned @drpatelh)
[x] ucsc/bigwigaverageoverbed (assigned @drpatelh)
[x] ucsc/wigtobigwig (assigned @drpatelh)
[x] unicycler (fixed by, or before, #1041)
[x] untar (assigned @drpatelh)
[x] unzip (assigned @drpatelh)
[x] vcftools (assigned @jfy133)
[x] yara/index (assigned @drpatelh)
[x] yara/mapper (assigned @grst: MD5sum mismatch on our HPC, works locally. Both with singularity. How is this even possible??)

drpatelh commented 3 years ago

The typical command used to run pytest has changed now. Don't forget to add NF_CORE_MODULES_TEST=1 to the beginning. We need to export that environment variable to be able to test the versions stuff.

Docker:

cd /path/to/git/clone/of/nf-core/modules/
NF_CORE_MODULES_TEST=1 PROFILE=docker pytest --tag fastqc --symlink --keep-workflow-wd

Singularity

cd /path/to/git/clone/of/nf-core/modules/
NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=singularity pytest --tag fastqc --symlink --keep-workflow-wd

grst commented 3 years ago

If anyone gets a FileNotFoundError for versions.yml like this one, then double-check that the workflow name in test.yml needs to start with the tool name.

FileNotFoundError: [Errno 2] No such file or directory: '/data/scratch/sturm/projects/2021/nf-core-modules-test-2/18/e188685ed693dac21be7e96d1ac8f3/pytest-workflow/Run_bismark_align_single-end_test_workflow/output/run/versions.yml'

/data/scratch/sturm/projects/2021/nf-core-modules-test-2/conda/nf-core-tools-dev-5bfdd78995f6a1657f45a07545dfe96b/lib/python3.8/pathlib.py:1078: FileNotFoundError

The fix of test.yml:

-- name: Run bismark align single-end test workflow
+- name: bismark align single-end test workflow

jfy133 commented 3 years ago

Note, updated profile command:

NF_CORE_MODULES_TEST=1 TMPDIR=/tmp/ PROFILE=singularity pytest tests/modules/fgbio/sortbam --symlink --wt 2 --keep-workflow-wd

from: https://nfcore.slack.com/archives/CJRH30T6V/p1632766640143300

muffato commented 1 year ago

The two tools that were as TODO actually got fixed a few weeks after

nf-core / modules