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[FEATURE] port pytest to nf-test for rnavar modules #3936

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35 tasks done
maxulysse opened this issue Oct 10, 2023 · 7 comments
Closed
35 tasks done

[FEATURE] port pytest to nf-test for rnavar modules #3936

maxulysse opened this issue Oct 10, 2023 · 7 comments
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@vlebars
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nf-test

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@maxulysse
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maxulysse commented Oct 10, 2023 •
edited by famosab
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Is your feature request related to a problem? Please describe

  • bedtools/merge
  • bedtools/sort
  • cat/fastq
  • custom/dumpsoftwareversions
  • ensemblvep/vep
  • fastqc
  • gatk4/applybqsr
  • gatk4/baserecalibrator
  • gatk4/bedtointervallist
  • gatk4/combinegvcfs
  • gatk4/createsequencedictionary
  • gatk4/haplotypecaller
  • gatk4/indexfeaturefile
  • gatk4/intervallisttools
  • gatk4/markduplicates
  • gatk4/mergevcfs
  • gatk4/splitncigarreads
  • gatk4/variantfiltration
  • gffread
  • gunzip
  • mosdepth
  • multiqc
  • samtools/faidx
  • samtools/flagstat
  • samtools/idxstats
  • samtools/index
  • samtools/merge
  • samtools/sort
  • samtools/stats
  • snpeff/snpeff
  • star/align
  • star/genomegenerate
  • tabix/bgziptabix
  • tabix/tabix
  • untar

Describe the solution you'd like

No response

Describe alternatives you've considered

No response

Additional context

No response
@maxulysse
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Note that we have overlap with #3935

@vlebars
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vlebars commented Mar 18, 2024

Hello ! I will work on samtools/faidx.

@vlebars vlebars self-assigned this Mar 18, 2024
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vlebars commented Mar 18, 2024

I will do bedtools/merge.

github-merge-queue bot pushed a commit that referenced this issue Mar 18, 2024
@vlebars @LouisLeNezet
add nf-test to samtools/faidx - #3936 (#5177)
aeb02a3 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
vlebars pushed a commit to vlebars/modules that referenced this issue Mar 18, 2024
add nf-test to bedtools/merge - nf-core#3936
7681cde
github-merge-queue bot pushed a commit that referenced this issue Mar 19, 2024
@vlebars
add nf-test to bedtools/merge - #3936 (#5203)
a537783 
Co-authored-by: LE BARS Victor <[email protected]>
@vlebars
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vlebars commented Mar 19, 2024

I will do bedtools/sort.

vlebars pushed a commit to vlebars/modules that referenced this issue Mar 19, 2024
add nf-test to bedtools/sort - nf-core#3936
eca3469
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vlebars commented Mar 19, 2024

I will do gatk4/bedtointervallist.

vlebars pushed a commit to vlebars/modules that referenced this issue Mar 19, 2024
add nf-test to gatk4/bedtointervallist - nf-core#3936
f49bcb2
vlebars pushed a commit to vlebars/modules that referenced this issue Mar 19, 2024
add nf-test to gatk4/bedtointervallist - nf-core#3936
b2e4166
jvfe added a commit to jvfe/modules that referenced this issue Mar 19, 2024
@jvfe
Merge branch 'master' into fastx_collapser
f7e851f 
* master:
  Added module ALE (nf-core#5211)
  add cram support to bowtie2 (nf-core#5180)
  Add nf-test to minimap2 index (nf-core#5189)
  nf-test all wisecondorx modules (nf-core#5219)
  splitncigarreads added meta for references (nf-core#5224)
  More tests for FASTQ_FASTQC_UMITOOLS_FASTP (nf-core#5179)
  SNPEFF_SNPEFF with nf-test tests (nf-core#5204)
  del extra info from config, passed sing and docker tests (nf-core#5217)
  Added meta map to module and tests (nf-core#5191)
  Nftest htseq (nf-core#5220)
  remove pytest files for `bcftools sort` (nf-core#5218)
  Cellpose: updated to 3.0.1 (nf-core#5193)
  rename taxonomy files in kraken2/add module (nf-core#5214)
  add nf-test to bedtools/merge - nf-core#3936 (nf-core#5203)
github-merge-queue bot pushed a commit that referenced this issue Mar 19, 2024
@vlebars
add nf-test to gatk4/bedtointervallist - #3936 (#5251)
d3f2158 
Co-authored-by: LE BARS Victor <[email protected]>
@vlebars
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vlebars commented Mar 19, 2024

I will do gatk4/combinegvcfs.

github-merge-queue bot pushed a commit that referenced this issue Mar 19, 2024
@vlebars @adamrtalbot
add nf-test to bedtools/sort - #3936 (#5221)
571a5fe 
* add nf-test to bedtools/sort - #3936

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
famosab pushed a commit to famosab/modules that referenced this issue Mar 19, 2024
@vlebars @famosab
add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)
2cb7c36 
Co-authored-by: LE BARS Victor <[email protected]>
jvfe added a commit to jvfe/modules that referenced this issue Mar 19, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
e16f6f9 
* master:
  Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. (nf-core#5278)
  added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158 (nf-core#5197)
  Update glimpse/phase output channel to phased_variants nf-core#5172 (nf-core#5174)
  Add module: GTFSORT (nf-core#5237)
  add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
  addedd optional output channel for lib files (nf-core#5257)
vlebars added a commit to vlebars/modules that referenced this issue Mar 20, 2024
@vlebars
add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)
8bdb60d 
Co-authored-by: LE BARS Victor <[email protected]>
vlebars added a commit to vlebars/modules that referenced this issue Mar 20, 2024
@vlebars @adamrtalbot
add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
745b01b 
* add nf-test to bedtools/sort - nf-core#3936

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
tucano pushed a commit to tucano/modules that referenced this issue Mar 20, 2024
@vlebars @LouisLeNezet @tucano
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
a9cc5d8 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
tucano pushed a commit to tucano/modules that referenced this issue Mar 20, 2024
@vlebars @tucano
add nf-test to bedtools/merge - nf-core#3936 (nf-core#5203)
d6e84b0 
Co-authored-by: LE BARS Victor <[email protected]>
tucano pushed a commit to tucano/modules that referenced this issue Mar 20, 2024
@vlebars @tucano
add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)
88ec758 
Co-authored-by: LE BARS Victor <[email protected]>
tucano pushed a commit to tucano/modules that referenced this issue Mar 20, 2024
@vlebars @adamrtalbot @tucano
add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
405fe20 
* add nf-test to bedtools/sort - nf-core#3936

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
github-merge-queue bot pushed a commit that referenced this issue Mar 20, 2024
@vlebars
add nf-test for gatk4/combinegvcfs - #3936 (#5337)
fe3d7aa 
add nf-test for gatk4/combinegvcfs

Co-authored-by: LE BARS Victor <[email protected]>
jvfe added a commit to jvfe/modules that referenced this issue Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
23cd668 
* master:
  add nf-test for gatk4/combinegvcfs - nf-core#3936 (nf-core#5337)
jennylsmith pushed a commit to RSC-RP/modules that referenced this issue Mar 20, 2024
@vlebars @LouisLeNezet @jennylsmith
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
9dc88ed 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this issue Mar 20, 2024
@vlebars @jennylsmith
add nf-test to bedtools/merge - nf-core#3936 (nf-core#5203)
aaa46b0 
Co-authored-by: LE BARS Victor <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this issue Mar 20, 2024
@vlebars @jennylsmith
add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)
2c100a9 
Co-authored-by: LE BARS Victor <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this issue Mar 20, 2024
@vlebars @adamrtalbot @jennylsmith
add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
578ebda 
* add nf-test to bedtools/sort - nf-core#3936

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this issue Mar 20, 2024
@vlebars @jennylsmith
add nf-test for gatk4/combinegvcfs - nf-core#3936 (nf-core#5337)
5fca928 
add nf-test for gatk4/combinegvcfs

Co-authored-by: LE BARS Victor <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this issue Mar 21, 2024
@vlebars @LouisLeNezet
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
37a8f02 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this issue Mar 21, 2024
@vlebars
add nf-test to bedtools/merge - nf-core#3936 (nf-core#5203)
3cdbf17 
Co-authored-by: LE BARS Victor <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this issue Mar 21, 2024
@vlebars
add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)
ac33de6 
Co-authored-by: LE BARS Victor <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this issue Mar 21, 2024
@vlebars @adamrtalbot
add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
f7093c0 
* add nf-test to bedtools/sort - nf-core#3936

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this issue Mar 21, 2024
@vlebars
add nf-test for gatk4/combinegvcfs - nf-core#3936 (nf-core#5337)
b4171d5 
add nf-test for gatk4/combinegvcfs

Co-authored-by: LE BARS Victor <[email protected]>
tucano pushed a commit to tucano/modules that referenced this issue Mar 22, 2024
@vlebars @tucano
add nf-test for gatk4/combinegvcfs - nf-core#3936 (nf-core#5337)
bdf3449 
add nf-test for gatk4/combinegvcfs

Co-authored-by: LE BARS Victor <[email protected]>
@famosab
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famosab commented Feb 13, 2025

All done :)

@famosab famosab closed this as completed Feb 13, 2025
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