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8 commits

Author SHA1 Message Date
Charles Plessy
894349b9b5
Fix 459 (#534)
* Update test data names.

Closes: #459

Thanks: @FriederikeHanssen

(`samtools` tests are already fixed by another commit)

* Fix file names in tests.

The update of test data name required changes in the test yml files.

I also updated the `bismark/summary/main.nf` file to get its data
from the `params.test_data` map.
2021-06-14 12:24:59 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389)
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
Patrick Hüther
3b1dcc9cc0
MethylDackel: fix version scraping (#401)
* methyldackel: fix version scraping

* fix output file path
2021-04-06 10:59:33 +01:00
Robert A. Petit III
c9256616b9
update tests for new config (#384)
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:22:06 +01:00
Harshil Patel
acb1a12a56
Re-organise all test data (#354)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Kevin Menden
4566525da2
Converge test data usage (#249)
* initial data restructuing

* fixed bedtools_complement

* fixed bedtools_genomecov

* fixed bedtools_getfasta

* fixed bedtools_intersect

* fixed bedtools maskfasta

* fixed bedtools_merge

* fixed bedtools_slop

* fixed bedtools_sort

* fixed bismark_genome_preparation

* fixed blast

* fixed bowtie data

* fixed bowtie2 data

* fixed bwa data

* fixed bwamem2 data usage

* fixed cat_fastq data

* fixed cutadapt data

* fixed dsh data

* fixed fastp data

* fixed fastqc; fixed bug with wrong fastq format

* fixed gatk

* fixed data for gffread, gunzip

* fixed ivar paths

* fixed data paths for minimap2

* fixed mosdepth

* fixed multiqc, pangolin

* fixed picard data paths

* fixed data paths for qualimap, quast

* fixed salmon data paths

* fixed samtools paths

* fixed seqwish, stringtie paths

* fixed tabix, trimgalore paths

* cleaned up data

* added first description to README

* changed test data naming again; everything up to bwa fixed

* everything up to gatk4

* fixed everything up to ivar

* fixed everything up to picard

* everything up to quast

* everything fixed up to stringtie

* switched everyting to 'test' naming scheme

* fixed samtools and ivar tests

* cleaned up README a bit

* add (simulated) methylation test data

based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90

* bwameth/align: update data paths and checksums

also, build index on the go

* bwameth/index: update data paths and checksums

* methyldackel/extract: update data paths and checksums

* methyldackel/mbias: update data paths and checksums

* bismark/deduplicate: update data paths and checksums

* remove obsolete testdata

* remove empty 'dummy_file.txt'

* update data/README.md

* methyldackel: fix test

* Revert "methyldackel: fix test"

This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a.

* methyldackel: fix test

for real

* move test.genome.sizes

* changed test names

* switched genomic to genome and transcriptome

* fix bedtools, blast

* fix gtf, tabix, .paf

* fix bowtie,bwa,bwameth

* fixed: bwa, bwamem, gatk, gffread, quast

* fixed bismark and blast

* fixed remaining tests

* delete bam file

Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00
phue
52b00d4286 add methyldackel/mbias + tests 2021-02-17 19:27:57 +01:00
phue
5ad7c6bc51 add methyldackel/extract + tests + testdata 2021-02-17 19:18:55 +01:00