From 13bd67ed8aca271a260c78ca41afe9e1f5c217d7 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Wed, 24 Mar 2021 19:29:41 +0100 Subject: [PATCH] Fix some module test after adapting test config approach (#379) * 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 --- tests/software/bowtie2/align/main.nf | 11 +++++----- tests/software/bowtie2/align/test.yml | 24 +++++++++++----------- tests/software/bowtie2/build_test/main.nf | 2 +- tests/software/bowtie2/build_test/test.yml | 12 +++++------ tests/software/bwameth/align/main.nf | 10 ++++----- tests/software/bwameth/index/main.nf | 2 +- tests/software/bwameth/index/test.yml | 12 +++++------ tests/software/multiqc/main.nf | 6 +++--- 8 files changed, 39 insertions(+), 40 deletions(-) diff --git a/tests/software/bowtie2/align/main.nf b/tests/software/bowtie2/align/main.nf index 3fcfe8fc..3f4883b7 100644 --- a/tests/software/bowtie2/align/main.nf +++ b/tests/software/bowtie2/align/main.nf @@ -7,9 +7,9 @@ include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addP workflow test_bowtie2_align_single_end { 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_ALIGN ( input, BOWTIE2_BUILD.out.index ) @@ -17,11 +17,10 @@ workflow test_bowtie2_align_single_end { workflow test_bowtie2_align_paired_end { input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_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_ALIGN ( input, BOWTIE2_BUILD.out.index ) } diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml index 8e246d88..1cb3d98b 100644 --- a/tests/software/bowtie2/align/test.yml +++ b/tests/software/bowtie2/align/test.yml @@ -7,17 +7,17 @@ files: - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/index/bowtie2/test_genome.3.bt2 + - path: ./output/index/bowtie2/genome.3.bt2 md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie2/test_genome.2.bt2 + - path: ./output/index/bowtie2/genome.2.bt2 md5sum: 47b153cd1319abc88dda532462651fcf - - path: ./output/index/bowtie2/test_genome.1.bt2 + - path: ./output/index/bowtie2/genome.1.bt2 md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf - - path: ./output/index/bowtie2/test_genome.4.bt2 + - path: ./output/index/bowtie2/genome.4.bt2 md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie2/test_genome.rev.1.bt2 + - path: ./output/index/bowtie2/genome.rev.1.bt2 md5sum: 52be6950579598a990570fbcf5372184 - - path: ./output/index/bowtie2/test_genome.rev.2.bt2 + - path: ./output/index/bowtie2/genome.rev.2.bt2 md5sum: e3b4ef343dea4dd571642010a7d09597 - name: bowtie2 align paired-end @@ -29,15 +29,15 @@ files: - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/index/bowtie2/test_genome.3.bt2 + - path: ./output/index/bowtie2/genome.3.bt2 md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie2/test_genome.2.bt2 + - path: ./output/index/bowtie2/genome.2.bt2 md5sum: 47b153cd1319abc88dda532462651fcf - - path: ./output/index/bowtie2/test_genome.1.bt2 + - path: ./output/index/bowtie2/genome.1.bt2 md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf - - path: ./output/index/bowtie2/test_genome.4.bt2 + - path: ./output/index/bowtie2/genome.4.bt2 md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie2/test_genome.rev.1.bt2 + - path: ./output/index/bowtie2/genome.rev.1.bt2 md5sum: 52be6950579598a990570fbcf5372184 - - path: ./output/index/bowtie2/test_genome.rev.2.bt2 + - path: ./output/index/bowtie2/genome.rev.2.bt2 md5sum: e3b4ef343dea4dd571642010a7d09597 diff --git a/tests/software/bowtie2/build_test/main.nf b/tests/software/bowtie2/build_test/main.nf index 33d0f434..206c1683 100644 --- a/tests/software/bowtie2/build_test/main.nf +++ b/tests/software/bowtie2/build_test/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] ) 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 ) } diff --git a/tests/software/bowtie2/build_test/test.yml b/tests/software/bowtie2/build_test/test.yml index 2c5bc1f9..96385860 100644 --- a/tests/software/bowtie2/build_test/test.yml +++ b/tests/software/bowtie2/build_test/test.yml @@ -4,15 +4,15 @@ - bowtie2 - bowtie2_build files: - - path: ./output/index/bowtie2/test_genome.3.bt2 + - path: ./output/index/bowtie2/genome.3.bt2 md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie2/test_genome.2.bt2 + - path: ./output/index/bowtie2/genome.2.bt2 md5sum: 47b153cd1319abc88dda532462651fcf - - path: ./output/index/bowtie2/test_genome.1.bt2 + - path: ./output/index/bowtie2/genome.1.bt2 md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf - - path: ./output/index/bowtie2/test_genome.4.bt2 + - path: ./output/index/bowtie2/genome.4.bt2 md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie2/test_genome.rev.1.bt2 + - path: ./output/index/bowtie2/genome.rev.1.bt2 md5sum: 52be6950579598a990570fbcf5372184 - - path: ./output/index/bowtie2/test_genome.rev.2.bt2 + - path: ./output/index/bowtie2/genome.rev.2.bt2 md5sum: e3b4ef343dea4dd571642010a7d09597 diff --git a/tests/software/bwameth/align/main.nf b/tests/software/bwameth/align/main.nf index a32fe02d..83f43a57 100644 --- a/tests/software/bwameth/align/main.nf +++ b/tests/software/bwameth/align/main.nf @@ -11,9 +11,9 @@ include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth */ workflow test_bwameth_align_single_end { 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_ALIGN_SE ( input, BWAMETH_INDEX.out.index ) @@ -24,10 +24,10 @@ workflow test_bwameth_align_single_end { */ workflow test_bwameth_align_paired_end { input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ] ] - fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) BWAMETH_INDEX ( fasta ) BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index ) diff --git a/tests/software/bwameth/index/main.nf b/tests/software/bwameth/index/main.nf index f41004d1..92e8ccd6 100644 --- a/tests/software/bwameth/index/main.nf +++ b/tests/software/bwameth/index/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] ) workflow test_bwameth_index { - fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) BWAMETH_INDEX ( fasta ) } diff --git a/tests/software/bwameth/index/test.yml b/tests/software/bwameth/index/test.yml index 662b79b8..79a53e50 100644 --- a/tests/software/bwameth/index/test.yml +++ b/tests/software/bwameth/index/test.yml @@ -4,15 +4,15 @@ - bwameth - bwameth_index files: - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t md5sum: 98039984526a41d04d6bd92fcc040c62 - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.pac + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.pac md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653 - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.amb + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.amb md5sum: 249a4195069071ce47cd0bae68abe376 - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.ann + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.ann md5sum: 46524d4359dcdfb203a235ab3b930dbb - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.bwt + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.bwt md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b - - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.sa + - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.sa md5sum: d25f6486f5134f57ed5b258f6fbb8673 diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf index b1d5218a..57a3f760 100644 --- a/tests/software/multiqc/main.nf +++ b/tests/software/multiqc/main.nf @@ -7,10 +7,10 @@ include { MULTIQC } from '../../../software/multiqc/main.nf' addParams( options: workflow test_multiqc { input = [ [ id: 'test', single_end: false ], - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] - + FASTQC ( input ) MULTIQC ( FASTQC.out.zip.collect { it[1] } ) }