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Fix some module test after adapting test config approach (#379)

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* Fix paths for bowtie2/build_test

* Fix paths for bowtie2/align

* Fix paths for bwameth/index

* Fix paths for bwameth/align

* Fix paths for multiqc tests
This commit is contained in:
Jose Espinosa-Carrasco 2021-03-24 19:29:41 +01:00 • committed by GitHub
parent 2dba72dd14
commit 13bd67ed8a
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GPG key ID: 4AEE18F83AFDEB23
8 changed files with 39 additions and 40 deletions
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11
tests/software/bowtie2/align/main.nf
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@ -7,9 +7,9 @@ include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addP
workflow test_bowtie2_align_single_end { workflow test_bowtie2_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
@ -17,11 +17,10 @@ workflow test_bowtie2_align_single_end {
workflow test_bowtie2_align_paired_end { workflow test_bowtie2_align_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_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)
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
} }

24
tests/software/bowtie2/align/test.yml
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@ -7,17 +7,17 @@
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
- path: ./output/index/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/index/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/index/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/index/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597
- name: bowtie2 align paired-end - name: bowtie2 align paired-end
@ -29,15 +29,15 @@
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
- path: ./output/index/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/index/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/index/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/index/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597

2
tests/software/bowtie2/build_test/main.nf
View file

@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] ) include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] )
workflow test_bowtie2_build { workflow test_bowtie2_build {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
} }

12
tests/software/bowtie2/build_test/test.yml
View file

@ -4,15 +4,15 @@
- bowtie2 - bowtie2
- bowtie2_build - bowtie2_build
files: files:
- path: ./output/index/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/index/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/index/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/index/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597

10
tests/software/bwameth/align/main.nf
View file

@ -11,9 +11,9 @@ include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth
*/ */
workflow test_bwameth_align_single_end { workflow test_bwameth_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta ) BWAMETH_INDEX ( fasta )
BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index ) BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
@ -24,10 +24,10 @@ workflow test_bwameth_align_single_end {
*/ */
workflow test_bwameth_align_paired_end { workflow test_bwameth_align_paired_end {
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)
BWAMETH_INDEX ( fasta ) BWAMETH_INDEX ( fasta )
BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index ) BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )

2
tests/software/bwameth/index/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] ) include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] )
workflow test_bwameth_index { workflow test_bwameth_index {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta ) BWAMETH_INDEX ( fasta )
} }

12
tests/software/bwameth/index/test.yml
View file

@ -4,15 +4,15 @@
- bwameth - bwameth
- bwameth_index - bwameth_index
files: files:
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t - path: ./output/index/bwameth/genome.fasta.bwameth.c2t
md5sum: 98039984526a41d04d6bd92fcc040c62 md5sum: 98039984526a41d04d6bd92fcc040c62
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.pac - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.pac
md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653 md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.amb - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.amb
md5sum: 249a4195069071ce47cd0bae68abe376 md5sum: 249a4195069071ce47cd0bae68abe376
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.ann - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.ann
md5sum: 46524d4359dcdfb203a235ab3b930dbb md5sum: 46524d4359dcdfb203a235ab3b930dbb
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.bwt - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.bwt
md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
- path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.sa - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.sa
md5sum: d25f6486f5134f57ed5b258f6fbb8673 md5sum: d25f6486f5134f57ed5b258f6fbb8673

6
tests/software/multiqc/main.nf
View file

@ -7,10 +7,10 @@ include { MULTIQC } from '../../../software/multiqc/main.nf' addParams( options:
workflow test_multiqc { workflow test_multiqc {
input = [ [ id: 'test', single_end: false ], input = [ [ id: 'test', single_end: false ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
FASTQC ( input ) FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] } ) MULTIQC ( FASTQC.out.zip.collect { it[1] } )
} }