From 9837ac7d7bb2e2362c021e8dc08efa96190b49a4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Sun, 4 Aug 2024 08:25:36 +1200 Subject: [PATCH] Updated test data paths batch 16 (#6102) Updated paths --- .../nf-core/abricate/run/tests/main.nf.test | 4 +-- modules/nf-core/abricate/summary/meta.yml | 4 +-- .../abricate/summary/tests/main.nf.test | 4 +-- modules/nf-core/angsd/gl/tests/main.nf.test | 32 +++++++++---------- modules/nf-core/bacphlip/tests/main.nf.test | 2 +- modules/nf-core/cellpose/tests/main.nf.test | 4 +-- .../hamronization/abricate/tests/main.nf.test | 4 +-- .../hamronization/deeparg/tests/main.nf.test | 4 +-- .../hamronization/fargene/tests/main.nf.test | 2 +- .../summarize/tests/main.nf.test | 4 +-- 10 files changed, 32 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/abricate/run/tests/main.nf.test b/modules/nf-core/abricate/run/tests/main.nf.test index 877bc3fa437..f31a67e7aed 100644 --- a/modules/nf-core/abricate/run/tests/main.nf.test +++ b/modules/nf-core/abricate/run/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - 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) ] input[1] = [] """ @@ -45,7 +45,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - 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) ] input[1] = [] """ diff --git a/modules/nf-core/abricate/summary/meta.yml b/modules/nf-core/abricate/summary/meta.yml index 390d0890732..71f1ac27605 100644 --- a/modules/nf-core/abricate/summary/meta.yml +++ b/modules/nf-core/abricate/summary/meta.yml @@ -17,7 +17,7 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - assembly: + - reports: type: file description: FASTA, GenBank or EMBL formatted file pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" @@ -31,7 +31,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - summary: + - report: type: file description: Tab-delimited report of aggregated results pattern: "*.{txt}" diff --git a/modules/nf-core/abricate/summary/tests/main.nf.test b/modules/nf-core/abricate/summary/tests/main.nf.test index 6e22191504c..a5423bd1f92 100644 --- a/modules/nf-core/abricate/summary/tests/main.nf.test +++ b/modules/nf-core/abricate/summary/tests/main.nf.test @@ -18,9 +18,9 @@ nextflow_process { """ input[0] = Channel.fromList([ tuple([ id:'test1', single_end:false ], // meta map - 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)), tuple([ id:'test2', single_end:false ], - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)) + file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)) ]) input[1] = [] """ diff --git a/modules/nf-core/angsd/gl/tests/main.nf.test b/modules/nf-core/angsd/gl/tests/main.nf.test index 412f46a53e8..3f8b0865649 100644 --- a/modules/nf-core/angsd/gl/tests/main.nf.test +++ b/modules/nf-core/angsd/gl/tests/main.nf.test @@ -18,11 +18,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -46,11 +46,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -74,11 +74,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -102,11 +102,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -132,11 +132,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -162,11 +162,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -192,11 +192,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ @@ -222,11 +222,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), ] input[1] = [ [ id:'test_fa' ], - 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[2] = [ [], [] ] """ diff --git a/modules/nf-core/bacphlip/tests/main.nf.test b/modules/nf-core/bacphlip/tests/main.nf.test index e3fddd7d884..4c3f1b8b7b5 100644 --- a/modules/nf-core/bacphlip/tests/main.nf.test +++ b/modules/nf-core/bacphlip/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true) // genome.fasta + file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true) // genome.fasta ] """ } diff --git a/modules/nf-core/cellpose/tests/main.nf.test b/modules/nf-core/cellpose/tests/main.nf.test index 1b6698d1d7e..6a7688baa8b 100644 --- a/modules/nf-core/cellpose/tests/main.nf.test +++ b/modules/nf-core/cellpose/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true) + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [] """ @@ -44,7 +44,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true) + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [] """ diff --git a/modules/nf-core/hamronization/abricate/tests/main.nf.test b/modules/nf-core/hamronization/abricate/tests/main.nf.test index 569ff942c92..d6c21350351 100644 --- a/modules/nf-core/hamronization/abricate/tests/main.nf.test +++ b/modules/nf-core/hamronization/abricate/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ] + input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] input[1] = 'tsv' input[2] = '1.0.1' input[3] = '2021-Mar-27' @@ -37,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ] + input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] input[1] = 'tsv' input[2] = '1.0.1' input[3] = '2021-Mar-27' diff --git a/modules/nf-core/hamronization/deeparg/tests/main.nf.test b/modules/nf-core/hamronization/deeparg/tests/main.nf.test index 88dd17008fc..e13be32872e 100644 --- a/modules/nf-core/hamronization/deeparg/tests/main.nf.test +++ b/modules/nf-core/hamronization/deeparg/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2' @@ -43,7 +43,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2' diff --git a/modules/nf-core/hamronization/fargene/tests/main.nf.test b/modules/nf-core/hamronization/fargene/tests/main.nf.test index 39fc6854813..a5c5f2f7dbe 100644 --- a/modules/nf-core/hamronization/fargene/tests/main.nf.test +++ b/modules/nf-core/hamronization/fargene/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { """ input[0] = Channel.fromList([ tuple([ id:'test', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)) + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)) ]) """ } diff --git a/modules/nf-core/hamronization/summarize/tests/main.nf.test b/modules/nf-core/hamronization/summarize/tests/main.nf.test index 0c3da24cf87..dc2da33e7f2 100644 --- a/modules/nf-core/hamronization/summarize/tests/main.nf.test +++ b/modules/nf-core/hamronization/summarize/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test1', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2' @@ -32,7 +32,7 @@ nextflow_process { """ input[0] = [ [ id:'test2', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2'