Commit graph

34 commits

Author SHA1 Message Date
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420)
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +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
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
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated (#336)
* Add default output dir for modules that create indices

* Change path for index module test output

* Fix bowtie2/align tests

* Fixing bowtie/align tests

* Fix genomegenerate test

* Fixing README linting
2021-03-23 17:55:01 +00:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds (#273)
* Fix bowtie  build test

* Forgot to delete old bowtie_build

* Fix bowtie2 build tests

* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
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
Harshil Patel
5aa920eb53
Update tests/software/bowtie/align/test.yml 2021-02-04 10:19:28 +00:00
Harshil Patel
68f9a0b711
Update tests/software/bowtie/build/test.yml 2021-02-04 10:08:01 +00:00
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _"
This reverts commit 9b454416d2.
2021-02-03 20:06:05 -06:00
Edmund Miller
9b454416d2
ci: Test bowtie-build instead of _ 2021-02-03 13:17:14 -06:00
Edmund Miller
7dbac4bdef
ci: Test adding another work to test name 2021-02-03 13:17:14 -06:00
Edmund Miller
b058da5856
ci: Test buil to see if build is special 2021-02-03 12:43:18 -06:00
Edmund Miller
4d58a037f6
test(bowtie_align): Fix md5sum 2021-02-03 12:37:19 -06:00
Edmund Miller
6901c7e830
ci: Fix bowtie_build names with "" 2021-02-03 12:37:14 -06:00
drpatelh
e71b3eaaa5 Rename workflows 2021-02-03 17:48:17 +00:00
drpatelh
a87d584c48 Change path to bowtie tests 2021-02-03 16:39:00 +00:00
drpatelh
9b153f296d Add check to see if bowtie bam files exists 2021-02-03 16:26:10 +00:00
drpatelh
239cbe17ad Fix relative paths 2021-02-03 16:20:02 +00:00
drpatelh
38c3ecfac6 Merge branch 'master' of https://github.com/nf-core/modules into split_tests 2021-02-03 16:05:06 +00:00
drpatelh
743ba37d4b Update filters paths 2021-02-03 16:04:43 +00:00
drpatelh
ff23473e82 Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00
drpatelh
8be5e05111 Remove bam md5sum check for bowtie 2021-02-03 13:46:44 +00:00
Edmund Miller
688cc05fe8
tests: Remove -profile in tests
See ddbca7b467 for more info
2021-02-02 15:30:59 -06:00
drpatelh
f84e5b59ca Rename bowtie_index to bowtie_build 2021-02-01 17:53:31 +00:00
kevinmenden
8f75bac67e update test.bam md5sums 2020-12-18 11:16:58 +01:00
kevinmenden
db0b631906 removed index from test output 2020-12-18 11:06:02 +01:00
kevinmenden
299a3fa07e adding .index back 2020-12-18 10:58:37 +01:00
kevinmenden
07f0a2476a fixed linting errors 2020-12-18 09:50:05 +01:00
kevinmenden
f35850bf14 bowtie bam output 2020-12-16 11:02:58 +01:00
kevinmenden
0d7c8276b7 added test yml and md5s 2020-12-09 16:54:11 +01:00
kevinmenden
42020ce5ac added tests for bowtie paired-end alignment; resolved index bug 2020-12-09 16:39:05 +01:00
kevinmenden
fee0707af1 added bowtie_align workflow test 2020-12-08 14:19:34 +01:00
kevinmenden
6660a597a3 added tests for bowtie module 2020-12-08 13:59:14 +01:00
kevinmenden
9d67da2b2c added module yml files 2020-12-08 13:40:32 +01:00