From ab80a04707104a4baf39341581dfbced5da05479 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 16 Aug 2024 17:41:52 +1200 Subject: [PATCH] Updated test data paths batch40 (#6196) --- .../tests/main.nf.test | 8 ++--- .../nf-core/bam_qc_picard/tests/main.nf.test | 34 +++++++++---------- .../tests/main.nf.test | 12 +++---- .../fastq_align_mapad/tests/main.nf.test | 6 ++-- .../mmseqs_contig_taxonomy/tests/main.nf.test | 2 +- 5 files changed, 31 insertions(+), 31 deletions(-) diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test index a330722420b..dd7f2371869 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test @@ -31,8 +31,8 @@ nextflow_workflow { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] """ @@ -45,7 +45,7 @@ nextflow_workflow { """ input[0] = [ [ id:'sarscov2'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -56,7 +56,7 @@ nextflow_workflow { """ input[0] = UMITOOLS_EXTRACT.out.reads input[1] = BWA_INDEX.out.index - input[2] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = true """ } diff --git a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test index 21a2630237a..10687889dec 100644 --- a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test @@ -18,22 +18,22 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ [ id:'test', single_end:false ], - 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [], [] ]) input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } @@ -72,22 +72,22 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ [ id:'test', single_end:false ], - 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']['genome']['baits_interval_list'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) ]) input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } @@ -129,22 +129,22 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ [ id:'test', single_end:false ], - 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [], [] ]) input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } diff --git a/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test b/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test index 6bc13bac745..d06617fb29c 100644 --- a/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test +++ b/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test @@ -23,11 +23,11 @@ nextflow_workflow { input[0] = Channel.of( [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ], [ [ id:'test2' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] ) input[1] = Channel.of( @@ -62,11 +62,11 @@ nextflow_workflow { input[0] = Channel.of( [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ], [ [ id:'test2' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] ) input[1] = Channel.of( @@ -97,11 +97,11 @@ nextflow_workflow { input[0] = Channel.of( [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ], [ [ id:'test2' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] ) input[1] = [] diff --git a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test index 841497c0f93..3d9d7575ef4 100644 --- a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_workflow { script "../../../../modules/nf-core/mapad/index/main.nf" process { """ - input[0] = [ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[0] = [ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] """ } } @@ -30,11 +30,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ]) input[1] = MAPAD_INDEX.out.index input[2] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[3] = 0.03 input[4] = false diff --git a/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test b/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test index 68853486223..5b5d58d92a0 100644 --- a/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test +++ b/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_workflow { """ input[0] = Channel.of([ [id:'bacteroides_fragilis'], - file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) ] ) """