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Move assembly test files from genome to illumina (#441)

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* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes

* Update test path in config for illumina assembly files

* Update modules using assembly files

* Correctly setting path of assembly files

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Jose Espinosa-Carrasco 2021-04-13 12:52:11 +02:00 committed by GitHub
parent 26fdebc8de
commit a9fcbd93cc
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 6 additions and 8 deletions
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10
tests/config/test_data.config
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@ -24,14 +24,8 @@ params {
kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2" kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz" kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas" all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas" informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
contigs_fasta = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/genome/scaffolds.fasta"
assembly_gfa = "${test_data_dir}/genomics/sarscov2/genome/assembly.gfa"
} }
'illumina' { 'illumina' {
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam" test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"
@ -66,6 +60,10 @@ params {
test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf" test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz" test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
contigs_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta"
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
} }
'nanopore' { 'nanopore' {
test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam" test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"

2
tests/software/abacas/main.nf
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@ -7,7 +7,7 @@ include { ABACAS } from '../../../software/abacas/main.nf' addParams ( options:
workflow test_abacas { workflow test_abacas {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['scaffolds_fasta'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

2
tests/software/plasmidid/main.nf
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@ -7,7 +7,7 @@ include { PLASMIDID } from '../../../software/plasmidid/main.nf' addParams ( opt
workflow test_plasmidid { workflow test_plasmidid {
contigs = [ [ id:'test' ], // meta map contigs = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['genome']['contigs_fasta'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)