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Code Issues Releases Packages Activity

update tests for new config (#384)

Browse source 
* 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>
This commit is contained in:
Robert A. Petit III 2021-04-01 15:22:06 -04:00 committed by GitHub
parent f126d980d7
commit c9256616b9
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GPG key ID: 4AEE18F83AFDEB23
21 changed files with 94 additions and 138 deletions
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1
tests/config/test_data.config
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@ -9,6 +9,7 @@ params {
genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai" genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict" genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3" genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf" genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes" genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta" transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"

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tests/data/genomics/sarscov2/genome/genome.gff3.gz Normal file
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2
tests/software/blast/blastn/main.nf
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@ -6,7 +6,7 @@ include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.
include { BLAST_BLASTN } from '../../../../software/blast/blastn/main.nf' addParams( options: [:] ) include { BLAST_BLASTN } from '../../../../software/blast/blastn/main.nf' addParams( options: [:] )
workflow test_blast_blastn { workflow test_blast_blastn {
input = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
BLAST_MAKEBLASTDB ( input ) BLAST_MAKEBLASTDB ( input )
BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db ) BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )

18
tests/software/blast/blastn/test.yml
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@ -5,18 +5,18 @@
- blast_blastn - blast_blastn
files: files:
- path: ./output/blast/test.blastn.txt - path: ./output/blast/test.blastn.txt
- path: ./output/blast/blast_db/test_genome.fasta.nsq - path: ./output/blast/blast_db/genome.fasta.nsq
md5sum: 982cbc7d9e38743b9b1037588862b9da md5sum: 982cbc7d9e38743b9b1037588862b9da
- path: ./output/blast/blast_db/test_genome.fasta.nin - path: ./output/blast/blast_db/genome.fasta.nin
- path: ./output/blast/blast_db/test_genome.fasta - path: ./output/blast/blast_db/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6 md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/blast/blast_db/test_genome.fasta.nhr - path: ./output/blast/blast_db/genome.fasta.nhr
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
- path: ./output/blast/blast_db/test_genome.fasta.ndb - path: ./output/blast/blast_db/genome.fasta.ndb
md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed md5sum: 45f2daf9769957ff80868dd3d80d30a3
- path: ./output/blast/blast_db/test_genome.fasta.not - path: ./output/blast/blast_db/genome.fasta.not
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
- path: ./output/blast/blast_db/test_genome.fasta.nto - path: ./output/blast/blast_db/genome.fasta.nto
md5sum: 33cdeccccebe80329f1fdbee7f5874cb md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- path: ./output/blast/blast_db/test_genome.fasta.ntf - path: ./output/blast/blast_db/genome.fasta.ntf
md5sum: 1f6027d443e67a98ad0edc2d39971b0c md5sum: 1f6027d443e67a98ad0edc2d39971b0c

2
tests/software/blast/makeblastdb/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] ) include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
workflow test_blast_makeblastdb { workflow test_blast_makeblastdb {
input = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
BLAST_MAKEBLASTDB ( input ) BLAST_MAKEBLASTDB ( input )
} }

18
tests/software/blast/makeblastdb/test.yml
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@ -4,18 +4,18 @@
- blast - blast
- blast_makeblastdb - blast_makeblastdb
files: files:
- path: ./output/blast/blast_db/test_genome.fasta.nsq - path: ./output/blast/blast_db/genome.fasta.nsq
md5sum: 982cbc7d9e38743b9b1037588862b9da md5sum: 982cbc7d9e38743b9b1037588862b9da
- path: ./output/blast/blast_db/test_genome.fasta.nin - path: ./output/blast/blast_db/genome.fasta.nin
- path: ./output/blast/blast_db/test_genome.fasta - path: ./output/blast/blast_db/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6 md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/blast/blast_db/test_genome.fasta.nhr - path: ./output/blast/blast_db/genome.fasta.nhr
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
- path: ./output/blast/blast_db/test_genome.fasta.ndb - path: ./output/blast/blast_db/genome.fasta.ndb
md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed md5sum: 45f2daf9769957ff80868dd3d80d30a3
- path: ./output/blast/blast_db/test_genome.fasta.not - path: ./output/blast/blast_db/genome.fasta.not
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
- path: ./output/blast/blast_db/test_genome.fasta.nto - path: ./output/blast/blast_db/genome.fasta.nto
md5sum: 33cdeccccebe80329f1fdbee7f5874cb md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- path: ./output/blast/blast_db/test_genome.fasta.ntf - path: ./output/blast/blast_db/genome.fasta.ntf
md5sum: 1f6027d443e67a98ad0edc2d39971b0c md5sum: 1f6027d443e67a98ad0edc2d39971b0c

4
tests/software/flash/main.nf
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@ -6,8 +6,8 @@ include { FLASH } from '../../../software/flash/main.nf' addParams( options: [ar
workflow test_flash { workflow test_flash {
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) ]
] ]
FLASH ( input ) FLASH ( input )

8
tests/software/methyldackel/extract/main.nf
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@ -6,10 +6,10 @@ 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("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
METHYLDACKEL_EXTRACT ( input, fasta, fai ) METHYLDACKEL_EXTRACT ( input, fasta, fai )
} }

9
tests/software/methyldackel/mbias/main.nf
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@ -6,11 +6,10 @@ 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("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
METHYLDACKEL_MBIAS ( input, fasta, fai ) METHYLDACKEL_MBIAS ( input, fasta, fai )
} }

4
tests/software/mosdepth/main.nf
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@ -6,8 +6,8 @@ include { MOSDEPTH } from '../../../software/mosdepth/main.nf' addParams( option
workflow test_mosdepth { workflow test_mosdepth {
input = [ [ id:'test', single_end:true ], input = [ [ id:'test', single_end:true ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ], [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
] ]
dummy = file("dummy_file.txt") dummy = file("dummy_file.txt")
window = 100 window = 100

4
tests/software/optitype/main.nf
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@ -2,11 +2,11 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { OPTITYPE } from ''../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] ) include { OPTITYPE } from '../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
workflow test_optitype { workflow test_optitype {
input = [ [ id:'test', seq_type:'dna' ], // meta map input = [ [ id:'test', seq_type:'dna' ], // meta map
file("${launchDir}/tests/data/genomics/homo_sapiens/illumina/bam/example_pe.bam", checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
OPTITYPE ( input ) OPTITYPE ( input )

2
tests/software/pangolin/main.nf
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@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( option
workflow test_pangolin { workflow test_pangolin {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] ] [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
PANGOLIN ( input ) PANGOLIN ( input )
} }

4
tests/software/qualimap/bamqc/main.nf
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@ -6,10 +6,10 @@ include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' ad
workflow test_qualimap_bamqc { workflow test_qualimap_bamqc {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
] ]
gff = file("dummy_file.txt") gff = file("dummy_file.txt")
use_gff = false use_gff = false
QUALIMAP_BAMQC ( input, gff, use_gff ) QUALIMAP_BAMQC ( input, gff, use_gff )
} }

8
tests/software/quast/main.nf
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@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:]) include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:])
workflow test_quast_ref { workflow test_quast_ref {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gff = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true) gff = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true) consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
use_fasta = true use_fasta = true
use_gtf = true use_gtf = true
@ -17,7 +17,7 @@ workflow test_quast_ref {
workflow test_quast_noref { workflow test_quast_noref {
fasta = file('fasta_dummy') fasta = file('fasta_dummy')
gff = file('gff_dummy') gff = file('gff_dummy')
consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
use_fasta = false use_fasta = false
use_gtf = false use_gtf = false

78
tests/software/quast/test.yml
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@ -6,32 +6,32 @@
files: files:
- path: ./output/quast/report.tsv - path: ./output/quast/report.tsv
- path: ./output/quast/quast/transposed_report.txt - path: ./output/quast/quast/transposed_report.txt
md5sum: 73ae4f7cbe0da640819214cb013a79ef md5sum: 5dee51af1e7f916200d0a80f0c66be60
- path: ./output/quast/quast/transposed_report.tex - path: ./output/quast/quast/transposed_report.tex
md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449 md5sum: 336ec8d7b403fe1e0519e3a39eadd691
- path: ./output/quast/quast/icarus.html - path: ./output/quast/quast/icarus.html
- path: ./output/quast/quast/transposed_report.tsv - path: ./output/quast/quast/transposed_report.tsv
md5sum: 475bf9987c421b72fe1675b54ae0bcbe md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
- path: ./output/quast/quast/report.tex - path: ./output/quast/quast/report.tex
md5sum: e4c1d12bfe94d5a10e2264397bb90f83 md5sum: a9aac7d2ac2263df7e4599e4431c7393
- path: ./output/quast/quast/report.txt - path: ./output/quast/quast/report.txt
md5sum: 6295e6d462b1db45b1bb9f3f508275ad md5sum: 2da78350f20819f2625bd467800700ad
- path: ./output/quast/quast/report.tsv - path: ./output/quast/quast/report.tsv
md5sum: b70404d2b4d4e905afcfe3d149a5bd15 md5sum: 38fb41afadc09ffcbef62e42fea49f5e
- path: ./output/quast/quast/report.html - path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf - path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log - path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/genome_stats/test_transcriptome_genomic_features_any.txt - path: ./output/quast/quast/genome_stats/transcriptome_genomic_features_any.txt
md5sum: 307b3bb1f42fc2f11a60a2e9846021d7 md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
- path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
- path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
- path: ./output/quast/quast/genome_stats/genome_info.txt - path: ./output/quast/quast/genome_stats/genome_info.txt
md5sum: a4bb1f2792c175fc8d7fbf37f219e552 md5sum: d0193b322079565dc78608291e9c44d1
- path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt - path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
md5sum: c52381f09ea40b6141be5232494727b6 md5sum: c52381f09ea40b6141be5232494727b6
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_transcriptome_GC_content_plot.pdf - path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/gc.icarus.txt - path: ./output/quast/quast/basic_stats/gc.icarus.txt
md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
- path: ./output/quast/quast/basic_stats/NGx_plot.pdf - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
@ -39,45 +39,45 @@
- path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
- path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.mis_contigs.info - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.unaligned.info - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
md5sum: a8505cf206bf53ca369f7e3073fee587 md5sum: a8505cf206bf53ca369f7e3073fee587
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
md5sum: 4895cb02a010f1db85fc4992ac3c63b1 md5sum: d778f337899736cc62ed837b739b375c
- path: ./output/quast/quast/contigs_reports/misassemblies_report.txt - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
md5sum: d5c9dd22ce8f382649f74ba1f61d8a84 md5sum: 8b9a6d675a41bab6bf344dde2a20a939
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
- path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
md5sum: c247152eb82b361106492642fd796e2c md5sum: c247152eb82b361106492642fd796e2c
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tex - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
md5sum: 0df52940978f10c0fc9ed5f6770f170e md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
- path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
md5sum: d83abdf60e7ef02354a783dff4262d7d md5sum: fdb440c653e2f0306286798cacceaadb
- path: ./output/quast/quast/contigs_reports/unaligned_report.tsv - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
md5sum: f2adf811a611abdcb9f10bd7801e61e1 md5sum: 81d9597314356363a6b4e0d67027345a
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
md5sum: dd6e08408ea9a6830d47d5c21b84d587 md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
- path: ./output/quast/quast/contigs_reports/unaligned_report.txt - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
md5sum: e77d87bafe0e2c881805f8dfcc5f2351 md5sum: a32a09a0df811d1a75fbfe124081d1ca
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
- path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
- path: ./output/quast/quast/contigs_reports/unaligned_report.tex - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0 md5sum: e8e3bcb86da2cbd8eded980de80fa45c
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
md5sum: ec9191d0acb5d5bce56b4842551a8598 md5sum: ec9191d0acb5d5bce56b4842551a8598
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
md5sum: dda3fc0addc41ecc0d5183dee6f95886 md5sum: dda3fc0addc41ecc0d5183dee6f95886
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.used_snps.gz - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.used_snps.gz
md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords_tmp - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
md5sum: ce66eaeb99fdc11e4d50efadc1816e04 md5sum: ce66eaeb99fdc11e4d50efadc1816e04
- path: ./output/quast/quast/icarus_viewers/alignment_viewer.html - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
@ -89,26 +89,26 @@
- quast_no_reference - quast_no_reference
files: files:
- path: ./output/quast/report.tsv - path: ./output/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa md5sum: 074e239aac0f298cf4cd2a28a9bb5690
- path: ./output/quast/quast/transposed_report.txt - path: ./output/quast/quast/transposed_report.txt
md5sum: 5496230d4bc3846616d7e08d52ffc081 md5sum: 8784d7c7349498e1507e09fbf554625d
- path: ./output/quast/quast/transposed_report.tex - path: ./output/quast/quast/transposed_report.tex
md5sum: cf6a3b50575b510a7c42f5e745dd8674 md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
- path: ./output/quast/quast/icarus.html - path: ./output/quast/quast/icarus.html
md5sum: ba0ddcdbcd743191d282e3986cb68735 md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
- path: ./output/quast/quast/transposed_report.tsv - path: ./output/quast/quast/transposed_report.tsv
md5sum: 4b128bbf595b07dd2e2d5230bf575d29 md5sum: f0b5f65b2050af83b6d170d384c7616b
- path: ./output/quast/quast/report.tex - path: ./output/quast/quast/report.tex
md5sum: ac22b93fad7cdb6a812e5f670e815647 md5sum: 3da038cc5a02ef83e225c5277b87970b
- path: ./output/quast/quast/report.txt - path: ./output/quast/quast/report.txt
md5sum: 283160faa1d8cd32064c49e3c6d738d5 md5sum: bd2faaef244f02aa072d544c0d6d6e71
- path: ./output/quast/quast/report.tsv - path: ./output/quast/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa md5sum: 074e239aac0f298cf4cd2a28a9bb5690
- path: ./output/quast/quast/report.html - path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf - path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log - path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_genome_GC_content_plot.pdf - path: ./output/quast/quast/basic_stats/genome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html

44
tests/software/spades/main.nf
View file

@ -1,44 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
workflow test_spades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
}
workflow test_spades_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
}
workflow test_coronospades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}
workflow test_coronospades_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) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}

2
tests/software/tabix/bgzip/main.nf
View file

@ -6,7 +6,7 @@ include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParam
workflow test_tabix_bgzip { workflow test_tabix_bgzip {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
] ]
TABIX_BGZIP ( input ) TABIX_BGZIP ( input )

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

@ -8,7 +8,7 @@ include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main
workflow test_tabix_tabix_bed { workflow test_tabix_tabix_bed {
input = [ [ id:'B.bed' ], // meta map input = [ [ id:'B.bed' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
] ]
TABIX_BED ( input ) TABIX_BED ( input )
@ -16,7 +16,7 @@ workflow test_tabix_tabix_bed {
workflow test_tabix_tabix_gff { workflow test_tabix_tabix_gff {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
] ]
TABIX_GFF ( input ) TABIX_GFF ( input )
@ -24,7 +24,7 @@ workflow test_tabix_tabix_gff {
workflow test_tabix_tabix_vcf { workflow test_tabix_tabix_vcf {
input = [ [ id:'test.vcf' ], // meta map input = [ [ id:'test.vcf' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
] ]
TABIX_VCF ( input ) TABIX_VCF ( input )

4
tests/software/tabix/tabix/test.yml
View file

@ -14,8 +14,8 @@
- tabix_tabix - tabix_tabix
- gff - gff
files: files:
- path: ./output/tabix/test_genome.gff3.gz.tbi - path: ./output/tabix/genome.gff3.gz.tbi
md5sum: 30de27e3f44662272cfe6b3093126ea6 md5sum: 4059fe4762568194cf293fc6df7b358b
- name: tabix tabix vcf - name: tabix tabix vcf
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
tags: tags:

8
tests/software/tiddit/sv/main.nf
View file

@ -6,17 +6,17 @@ include { TIDDIT_SV } from '../../../../software/tiddit/sv/main.nf' addParams( o
workflow test_tiddit_sv { workflow test_tiddit_sv {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
TIDDIT_SV ( input, fasta, fai ) TIDDIT_SV ( input, fasta, fai )
} }
workflow test_tiddit_sv_no_ref { workflow test_tiddit_sv_no_ref {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
] ]
TIDDIT_SV ( input, [], [] ) TIDDIT_SV ( input, [], [] )

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

@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
workflow test_unicycler_single_end { workflow test_unicycler_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
UNICYCLER ( input ) UNICYCLER ( input )
@ -14,8 +14,8 @@ workflow test_unicycler_single_end {
workflow test_unicycler_paired_end { workflow test_unicycler_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
UNICYCLER ( input ) UNICYCLER ( input )