millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Fix 459 (#534)

Browse source 
* 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.
This commit is contained in:
Charles Plessy 2021-06-14 20:24:59 +09:00 committed by GitHub
parent 01dc6a289d
commit 894349b9b5
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
12 changed files with 35 additions and 36 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

12
tests/software/bismark/align/test.yml
View file

@ -4,9 +4,9 @@
- bismark - bismark
- bismark/align - bismark/align
files: files:
- path: output/test_single_end/test_methylated_1_bismark_bt2.bam - path: output/test_single_end/test.methylated_1_bismark_bt2.bam
md5sum: 7f9744cec5aa7908675e5fae79af36fc md5sum: dca4ba9ff705b70446f812e59bdb1a32
- path: output/test_single_end/test_methylated_1_bismark_bt2_SE_report.txt - path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
- name: Run bismark align paired-end test workflow - name: Run bismark align paired-end test workflow
command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
@ -14,6 +14,6 @@
- bismark - bismark
- bismark/align - bismark/align
files: files:
- path: output/test_paired_end/test_methylated_1_bismark_bt2_pe.bam - path: output/test_paired_end/test.methylated_1_bismark_bt2_pe.bam
md5sum: b13d0d40dffd336375f80fc94acc295f md5sum: 43943b1f30d056fcbd9ed26061ea0583
- path: output/test_paired_end/test_methylated_1_bismark_bt2_PE_report.txt - path: output/test_paired_end/test.methylated_1_bismark_bt2_PE_report.txt

2
tests/software/bismark/deduplicate/main.nf
View file

@ -6,7 +6,7 @@ include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/m
workflow test_bismark_deduplicate { workflow test_bismark_deduplicate {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
] ]
BISMARK_DEDUPLICATE ( input ) BISMARK_DEDUPLICATE ( input )

7
tests/software/bismark/deduplicate/test.yml
View file

@ -4,6 +4,7 @@
- bismark - bismark
- bismark/deduplicate - bismark/deduplicate
files: files:
- path: output/bismark/test_methylated_paired_end.deduplicated.bam - path: output/bismark/test.paired_end.methylated.deduplicated.bam
- path: output/bismark/test_methylated_paired_end.deduplication_report.txt md5sum: 82213a207048bcb5d8cc1cee92703a29
md5sum: 3876d694f10c58f47e380ba8476a356b - path: output/bismark/test.paired_end.methylated.deduplication_report.txt
md5sum: 86aaf87bac9ccdc3cc83628f20b902dc

2
tests/software/bismark/methylationextractor/main.nf
View file

@ -7,7 +7,7 @@ include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/meth
workflow test_bismark_methylationextractor { workflow test_bismark_methylationextractor {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

20
tests/software/bismark/methylationextractor/test.yml
View file

@ -4,15 +4,13 @@
- bismark - bismark
- bismark/methylationextractor - bismark/methylationextractor
files: files:
- path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz - path: output/bismark/CHG_OB_test.paired_end.methylated.txt.gz
- path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz - path: output/bismark/CHG_OT_test.paired_end.methylated.txt.gz
- path: output/bismark/CHH_OB_test_methylated_paired_end.txt.gz - path: output/bismark/CHH_OB_test.paired_end.methylated.txt.gz
- path: output/bismark/CHH_OT_test_methylated_paired_end.txt.gz - path: output/bismark/CHH_OT_test.paired_end.methylated.txt.gz
- path: output/bismark/CpG_OB_test_methylated_paired_end.txt.gz - path: output/bismark/CpG_OB_test.paired_end.methylated.txt.gz
- path: output/bismark/CpG_OT_test_methylated_paired_end.txt.gz - path: output/bismark/CpG_OT_test.paired_end.methylated.txt.gz
- path: output/bismark/test_methylated_paired_end.bedGraph.gz - path: output/bismark/test.paired_end.methylated.M-bias.txt
- path: output/bismark/test_methylated_paired_end.bismark.cov.gz
- path: output/bismark/test_methylated_paired_end.M-bias.txt
md5sum: 0b100924d46b3c35115f1206f34c4a59 md5sum: 0b100924d46b3c35115f1206f34c4a59
- path: output/bismark/test_methylated_paired_end_splitting_report.txt - path: output/bismark/test.paired_end.methylated_splitting_report.txt
md5sum: 288d6f0110127e3a8c10391802118202 md5sum: f28a9dd8de8c42b8900b190b8f79647a

4
tests/software/bismark/report/test.yml
View file

@ -4,5 +4,5 @@
- bismark - bismark
- bismark/report - bismark/report
files: files:
- path: output/bismark/test_methylated_1_bismark_bt2_PE_report.txt - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.html
- path: output/bismark/test_methylated_1_bismark_bt2_PE_report.html - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt

6
tests/software/bismark/summary/main.nf
View file

@ -10,10 +10,10 @@ include { BISMARK_SUMMARY } from '../../../../software/bismark/summ
workflow test_bismark_summary { workflow test_bismark_summary {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index ) BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )

2
tests/software/bismark/summary/test.yml
View file

@ -6,4 +6,4 @@
files: files:
- path: output/bismark/bismark_summary_report.html - path: output/bismark/bismark_summary_report.html
- path: output/bismark/bismark_summary_report.txt - path: output/bismark/bismark_summary_report.txt
md5sum: 06fc717e81b3f8f0d6e279d572f407f6 md5sum: fdfadd5399c4e7b2108da100e72036eb

4
tests/software/methyldackel/extract/main.nf
View file

@ -6,8 +6,8 @@ include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract
workflow test_methyldackel_extract { workflow test_methyldackel_extract {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

4
tests/software/methyldackel/extract/test.yml
View file

@ -4,5 +4,5 @@
- methyldackel - methyldackel
- methyldackel/extract - methyldackel/extract
files: files:
- path: output/methyldackel/test_methylated_paired_end.sorted_CpG.bedGraph - path: output/methyldackel/test.paired_end.methylated.sorted_CpG.bedGraph
md5sum: d7c637e2ef20de401fc610206f6bf6b7 md5sum: abcc9d1db6e48d5aced567c337b563d4

4
tests/software/methyldackel/mbias/main.nf
View file

@ -6,8 +6,8 @@ include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/mai
workflow test_methyldackel_mbias { workflow test_methyldackel_mbias {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

4
tests/software/msisensor/msi/main.nf
View file

@ -20,8 +20,8 @@ workflow test_msisensor_msi {
def input = [] def input = []
input = Channel.from([ [ id:'test', single_end:false ], // meta map input = Channel.from([ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ])
//scan.txt.view() //scan.txt.view()