update tests for new config (#384)

* 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>

tests/config/test_data.config

@@ -9,6 +9,7 @@ params {
                 genome_fasta_fai                          = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
                 genome_dict                               = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
                 genome_gff3                               = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
+                genome_gff3_gz                            = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
                 genome_gtf                                = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
                 genome_sizes                              = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
                 transcriptome_fasta                       = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"

tests/software/blast/blastn/main.nf

@@ -6,7 +6,7 @@ include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.
 include { BLAST_BLASTN      } from '../../../../software/blast/blastn/main.nf'      addParams( options: [:] )
 
 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_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )

tests/software/blast/blastn/test.yml

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

tests/software/blast/makeblastdb/main.nf

@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
 
 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 )
 }

tests/software/blast/makeblastdb/test.yml

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

tests/software/flash/main.nf

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

tests/software/methyldackel/extract/main.nf

@@ -6,10 +6,10 @@ include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract
 
 workflow test_methyldackel_extract {
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    fai   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], 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)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     METHYLDACKEL_EXTRACT ( input, fasta, fai )
 }

tests/software/methyldackel/mbias/main.nf

@@ -6,11 +6,10 @@ include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/mai
 
 workflow test_methyldackel_mbias {
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) 
-            ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    fai   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], 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)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     METHYLDACKEL_MBIAS ( input, fasta, fai )
 }

tests/software/mosdepth/main.nf

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

tests/software/optitype/main.nf

@@ -2,11 +2,11 @@
 
 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 {
     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 )

tests/software/pangolin/main.nf

@@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( option
 
 workflow test_pangolin {
     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 )
 }

tests/software/qualimap/bamqc/main.nf

@@ -6,10 +6,10 @@ include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' ad
 
 workflow test_qualimap_bamqc {
     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")
     use_gff = false
 
     QUALIMAP_BAMQC ( input, gff, use_gff )
-}
+}

tests/software/quast/main.nf

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

tests/software/quast/test.yml

@@ -6,32 +6,32 @@
   files:
     - path: ./output/quast/report.tsv
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 73ae4f7cbe0da640819214cb013a79ef
+      md5sum: 5dee51af1e7f916200d0a80f0c66be60
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449
+      md5sum: 336ec8d7b403fe1e0519e3a39eadd691
     - path: ./output/quast/quast/icarus.html
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 475bf9987c421b72fe1675b54ae0bcbe
+      md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
     - path: ./output/quast/quast/report.tex
-      md5sum: e4c1d12bfe94d5a10e2264397bb90f83
+      md5sum: a9aac7d2ac2263df7e4599e4431c7393
     - path: ./output/quast/quast/report.txt
-      md5sum: 6295e6d462b1db45b1bb9f3f508275ad
+      md5sum: 2da78350f20819f2625bd467800700ad
     - path: ./output/quast/quast/report.tsv
-      md5sum: b70404d2b4d4e905afcfe3d149a5bd15
+      md5sum: 38fb41afadc09ffcbef62e42fea49f5e
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - 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
     - 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/genome_info.txt
-      md5sum: a4bb1f2792c175fc8d7fbf37f219e552
-    - path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt
+      md5sum: d0193b322079565dc78608291e9c44d1
+    - path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
       md5sum: c52381f09ea40b6141be5232494727b6
     - path: ./output/quast/quast/basic_stats/cumulative_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
       md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
     - 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/NGAx_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
     - 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
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
-      md5sum: 4895cb02a010f1db85fc4992ac3c63b1
+      md5sum: d778f337899736cc62ed837b739b375c
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
-      md5sum: d5c9dd22ce8f382649f74ba1f61d8a84
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout
-    - path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv
+      md5sum: 8b9a6d675a41bab6bf344dde2a20a939
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
+    - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
       md5sum: c247152eb82b361106492642fd796e2c
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
-      md5sum: 0df52940978f10c0fc9ed5f6770f170e
-    - path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa
+      md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
+    - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
-      md5sum: d83abdf60e7ef02354a783dff4262d7d
+      md5sum: fdb440c653e2f0306286798cacceaadb
     - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
-      md5sum: f2adf811a611abdcb9f10bd7801e61e1
+      md5sum: 81d9597314356363a6b4e0d67027345a
     - 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/misassemblies_report.tsv
-      md5sum: e77d87bafe0e2c881805f8dfcc5f2351
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr
+      md5sum: a32a09a0df811d1a75fbfe124081d1ca
+    - 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/unaligned_report.tex
-      md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered
+      md5sum: e8e3bcb86da2cbd8eded980de80fa45c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
       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
-    - 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
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
       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
     - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
@@ -89,26 +89,26 @@
     - quast_no_reference
   files:
     - path: ./output/quast/report.tsv
-      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
+      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 5496230d4bc3846616d7e08d52ffc081
+      md5sum: 8784d7c7349498e1507e09fbf554625d
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: cf6a3b50575b510a7c42f5e745dd8674
+      md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
     - path: ./output/quast/quast/icarus.html
-      md5sum: ba0ddcdbcd743191d282e3986cb68735
+      md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 4b128bbf595b07dd2e2d5230bf575d29
+      md5sum: f0b5f65b2050af83b6d170d384c7616b
     - path: ./output/quast/quast/report.tex
-      md5sum: ac22b93fad7cdb6a812e5f670e815647
+      md5sum: 3da038cc5a02ef83e225c5277b87970b
     - path: ./output/quast/quast/report.txt
-      md5sum: 283160faa1d8cd32064c49e3c6d738d5
+      md5sum: bd2faaef244f02aa072d544c0d6d6e71
     - path: ./output/quast/quast/report.tsv
-      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
+      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - path: ./output/quast/quast/quast.log
     - path: ./output/quast/quast/basic_stats/cumulative_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/icarus_viewers/contig_size_viewer.html

tests/software/spades/main.nf

@@ -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 )
-}
-

tests/software/tabix/bgzip/main.nf

@@ -6,7 +6,7 @@ include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParam
 
 workflow test_tabix_bgzip {
     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 )

tests/software/tabix/tabix/main.nf

@@ -8,7 +8,7 @@ include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main
 
 workflow test_tabix_tabix_bed {
     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 )
@@ -16,7 +16,7 @@ workflow test_tabix_tabix_bed {
 
 workflow test_tabix_tabix_gff {
     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 )
@@ -24,7 +24,7 @@ workflow test_tabix_tabix_gff {
 
 workflow test_tabix_tabix_vcf {
     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 )

tests/software/tabix/tabix/test.yml

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

tests/software/tiddit/sv/main.nf

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

tests/software/unicycler/main.nf

@@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
 
 workflow test_unicycler_single_end {
     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 )
@@ -14,8 +14,8 @@ workflow test_unicycler_single_end {
 
 workflow test_unicycler_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) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
             ]
 
     UNICYCLER ( input )