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nf-core_modules/tests/config/pytest_modules.yml
Sébastien Guizard 4ec8b025bd
New module: LIMA (#719) 
* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 🐛 FIX: Clean test_data.config

* Update modules/lima/main.nf

Add meta to each output

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/lima/main.nf

Remove useless parenthesis

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* 🐛 FIX: Keep version number only

* 🐛 FIX: Reintegrate prefix variable and use it to define output file name

* 👌 IMPROVE: add suffix arg to check output files names

* 👌 IMPROVE: Use prefix for output filename

* 🐛 FIX: Set optional output

Allow usage of different input formats

* 👌 IMPROVE: Update meta file

* 👌 IMPROVE: Update test

One test for each input file type

* 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files

* 👌 IMPROVE: Update with last templates / Follow new version.yaml rule

* 🐛 FIX: Fix typos and include getProcessName function

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Using suffix to manage output was not a my best idea

Add a bash code to detect extension and update output file name

* 👌 IMPROVE: clean code

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-09-27 16:14:35 +01:00

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abacas:
- modules/abacas/**
- tests/modules/abacas/**
adapterremoval:
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agrvate:
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allelecounter:
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arriba:
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bowtie/align:
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bwa/aln:
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bwa/index:
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bwa/mem:
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bwa/sampe:
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bwa/samse:
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cat/cat:
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chromap/chromap:
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cnvkit:
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cooler/digest:
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cooler/dump:
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cutadapt:
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damageprofiler:
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deeptools/computematrix:
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deeptools/plotfingerprint:
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deeptools/plotheatmap:
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deeptools/plotprofile:
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delly/call:
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diamond/blastx:
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diamond/blastp:
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diamond/makedb:
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dragonflye:
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dshbio/filterbed:
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dshbio/splitbed:
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dshbio/splitgff3:
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ensemblvep:
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expansionhunter:
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fastani:
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fastp:
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fastqc:
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fasttree:
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fgbio/callmolecularconsensusreads:
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- tests/modules/fgbio/callmolecularconsensusreads/**
fgbio/sortbam:
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flash:
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gatk4/applybqsr:
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gatk4/baserecalibrator:
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gatk4/bedtointervallist:
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gatk4/createsequencedictionary:
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gatk4/fastqtosam:
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gatk4/getpileupsummaries:
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gatk4/haplotypecaller:
- modules/gatk4/haplotypecaller/**
- tests/modules/gatk4/haplotypecaller/**
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
gatk4/markduplicates:
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gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
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gatk4/mutect2:
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gatk4/revertsam:
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gatk4/samtofastq:
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gatk4/splitncigarreads:
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gatk4/variantfiltration:
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gffread:
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glnexus:
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graphmap2/align:
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gubbins:
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gunzip:
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hifiasm:
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hisat2/align:
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- modules/hisat2/extractsplicesites/**
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hisat2/build:
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hisat2/extractsplicesites:
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hmmer/hmmalign:
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homer/annotatepeaks:
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- tests/modules/homer/annotatepeaks/**
homer/findpeaks:
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homer/maketagdirectory:
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homer/makeucscfile:
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iqtree:
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ivar/consensus:
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ivar/trim:
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ivar/variants:
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kallisto/index:
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kallistobustools/count:
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kallistobustools/ref:
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kleborate:
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kraken2/kraken2:
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last/dotplot:
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last/lastal:
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last/lastdb:
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last/mafconvert:
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last/mafswap:
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last/postmask:
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last/split:
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last/train:
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lima:
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lofreq/call:
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lofreq/callparallel:
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lofreq/filter:
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lofreq/indelqual:
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malt/build:
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malt/run:
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maltextract:
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mash/sketch:
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metaphlan3:
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methyldackel/extract:
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methyldackel/mbias:
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minia:
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msisensor/scan:
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multiqc:
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muscle:
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nanolyse:
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nanoplot:
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nextclade:
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optitype:
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pairix:
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pairtools/dedup:
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pairtools/flip:
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pairtools/parse:
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pairtools/restrict:
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pairtools/select:
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pairtools/sort:
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pangolin:
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pbccs:
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picard/collectmultiplemetrics:
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picard/collectwgsmetrics:
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picard/filtersamreads:
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picard/markduplicates:
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picard/mergesamfiles:
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picard/sortsam:
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plasmidid:
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plink/vcf:
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preseq/lcextrap:
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prodigal:
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prokka:
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pycoqc:
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pydamage/analyze:
- modules/pydamage/analyze/**
- tests/modules/pydamage/analyze/**
pydamage/filter:
- modules/pydamage/filter/**
- tests/modules/pydamage/filter/**
qcat:
- modules/qcat/**
- tests/modules/qcat/**
qualimap/bamqc:
- modules/qualimap/bamqc/**
- tests/modules/qualimap/bamqc/**
quast:
- modules/quast/**
- tests/modules/quast/**
rapidnj:
- modules/rapidnj/**
- tests/modules/rapidnj/**
rasusa:
- modules/rasusa/**
- tests/modules/rasusa/**
raxmlng:
- modules/raxmlng/**
- tests/modules/raxmlng/**
rsem/calculateexpression:
- modules/rsem/calculateexpression/**
- tests/modules/rsem/calculateexpression/**
rsem/preparereference:
- modules/rsem/preparereference/**
- tests/modules/rsem/preparereference/**
rseqc/bamstat:
- modules/rseqc/bamstat/**
- tests/modules/rseqc/bamstat/**
rseqc/inferexperiment:
- modules/rseqc/inferexperiment/**
- tests/modules/rseqc/inferexperiment/**
rseqc/innerdistance:
- modules/rseqc/innerdistance/**
- tests/modules/rseqc/innerdistance/**
rseqc/junctionannotation:
- modules/rseqc/junctionannotation/**
- tests/modules/rseqc/junctionannotation/**
rseqc/junctionsaturation:
- modules/rseqc/junctionsaturation/**
- tests/modules/rseqc/junctionsaturation/**
rseqc/readdistribution:
- modules/rseqc/readdistribution/**
- tests/modules/rseqc/readdistribution/**
rseqc/readduplication:
- modules/rseqc/readduplication/**
- tests/modules/rseqc/readduplication/**
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
samtools/ampliconclip:
- modules/samtools/ampliconclip/**
- tests/modules/samtools/ampliconclip/**
samtools/faidx:
- modules/samtools/faidx/**
- tests/modules/samtools/faidx/**
samtools/fastq:
- modules/samtools/fastq/**
- tests/modules/samtools/fastq/**
samtools/flagstat:
- modules/samtools/flagstat/**
- tests/modules/samtools/flagstat/**
samtools/idxstats:
- modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/**
samtools/index:
- modules/samtools/index/**
- tests/modules/samtools/index/**
samtools/merge:
- modules/samtools/merge/**
- tests/modules/samtools/merge/**
samtools/mpileup:
- modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/**
samtools/sort:
- modules/samtools/sort/**
- tests/modules/samtools/sort/**
samtools/stats:
- modules/samtools/stats/**
- tests/modules/samtools/stats/**
samtools/view:
- modules/samtools/view/**
- tests/modules/samtools/view/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
seqtk/sample:
- modules/seqtk/sample/**
- tests/modules/seqtk/sample/**
seqtk/subseq:
- modules/seqtk/subseq/**
- tests/modules/seqtk/subseq/**
sequenzautils/bam2seqz:
- modules/sequenzautils/bam2seqz/**
- tests/modules/sequenzautils/bam2seqz/**
sequenzautils/gcwiggle:
- modules/sequenzautils/gcwiggle/**
- tests/modules/sequenzautils/gcwiggle/**
seqwish/induce:
- modules/seqwish/induce/**
- tests/modules/seqwish/induce/**
shovill:
- modules/shovill/**
- tests/modules/shovill/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
snpeff:
- modules/snpeff/**
- tests/modules/snpeff/**
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
spades:
- modules/spades/**
- tests/modules/spades/**
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**
star/align:
- modules/star/align/**
- tests/modules/star/align/**
star/genomegenerate:
- modules/star/genomegenerate/**
- tests/modules/star/genomegenerate/**
strelka/germline:
- modules/strelka/germline/**
- tests/modules/strelka/germline/**
stringtie/merge:
- modules/stringtie/merge/**
- tests/modules/stringtie/merge/**
stringtie/stringtie:
- modules/stringtie/stringtie/**
- tests/modules/stringtie/stringtie/**
subread/featurecounts:
- modules/subread/featurecounts/**
- tests/modules/subread/featurecounts/**
tabix/bgzip:
- modules/tabix/bgzip/**
- tests/modules/tabix/bgzip/**
tabix/bgziptabix:
- modules/tabix/bgziptabix/**
- tests/modules/tabix/bgziptabix/**
tabix/tabix:
- modules/tabix/tabix/**
- tests/modules/tabix/tabix/**
tiddit/sv:
- modules/tiddit/sv/**
- tests/modules/tiddit/sv/**
trimgalore:
- modules/trimgalore/**
- tests/modules/trimgalore/**
ucsc/bed12tobigbed:
- modules/ucsc/bed12tobigbed/**
- tests/modules/ucsc/bed12tobigbed/**
ucsc/bedclip:
- modules/ucsc/bedclip/**
- tests/modules/ucsc/bedclip/**
ucsc/bedgraphtobigwig:
- modules/ucsc/bedgraphtobigwig/**
- tests/modules/ucsc/bedgraphtobigwig/**
ucsc/bigwigaverageoverbed:
- modules/ucsc/bigwigaverageoverbed/**
- tests/modules/ucsc/bigwigaverageoverbed/**
ucsc/wigtobigwig:
- modules/ucsc/wigtobigwig/**
- tests/modules/ucsc/wigtobigwig/**
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**
untar:
- modules/untar/**
- tests/modules/untar/**
unzip:
- modules/unzip/**
- tests/modules/unzip/**
variantbam:
- modules/variantbam/**
- tests/modules/variantbam/**
vcftools:
- modules/vcftools/**
- tests/modules/vcftools/**
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**
yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**
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