Moved file for profile test_full

Plant-Food-Research-Open · Feb 27, 2024 · efdac55 · efdac55
1 parent 27b746f
commit efdac55
Show file tree

Hide file tree

Showing 6 changed files with 37 additions and 15 deletions.
diff --git a/assets/assemblysheet.csv b/assets/assemblysheet.csv
@@ -1,2 +1,2 @@
 tag,fasta,gff3,monoploid_ids,synteny_labels
-FI1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.gff.gz,,
+FI1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.gff.gz,https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/tests/stub/FI1.monoploid.seqs.txt,https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/tests/stub/FI1.seq.labels.tsv
diff --git a/tests/stub/xrefsheet.csv → assets/xrefsheet.csv b/tests/stub/xrefsheet.csv → assets/xrefsheet.csv
diff --git a/conf/test.config b/conf/test.config
@@ -11,13 +11,13 @@
 */
 
 params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name         = 'Test profile'
+    config_profile_description  = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+    input                       = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/assemblysheet.csv'
 
-    input = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/assemblysheet.csv'
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus                    = 2
+    max_memory                  = '6.GB'
+    max_time                    = '6.h'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -11,8 +11,32 @@
 */
 
 params {
-    config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name         = 'Full test profile'
+    config_profile_description  = 'Full test dataset to check pipeline function'
 
-    input = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/assemblysheet.csv'
+    input                       = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/assemblysheet.csv'
+
+    ncbi_fcs_adaptor_skip       = false
+    ncbi_fcs_adaptor_empire     = 'euk'
+
+    ncbi_fcs_gx_skip            = true // Skipping this step as the dataset is humengous (500 GB). Please download the dataset manually
+    // ncbi_fcs_gx_tax_id       = 35717
+    // ncbi_fcs_gx_db_path      = 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2023-01-24'
+
+    busco_skip                  = false
+    busco_mode                  = 'geno'
+    busco_lineage_datasets      = 'fungi_odb10 hypocreales_odb10'
+
+    tidk_skip                   = false
+    tidk_repeat_seq             = 'TTTGGG'
+
+    lai_skip                    = false
+
+    kraken2_skip                = true // Skipping this step as the dataset is humengous (126 GB). Please download the dataset manually
+    // kraken2_db_path          = 'https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz'
+
+    hic                         = 'SRR8238190'
+
+    synteny_skip                = false
+    synteny_xref_assemblies     = 'tests/stub/xrefsheet.csv'
 }
diff --git a/tests/stub/assemblysheet.csv b/tests/stub/assemblysheet.csv
diff --git a/tests/stub/stub.config b/tests/stub/stub.config
@@ -2,7 +2,7 @@ params {
     config_profile_name         = 'Full stub test'
     config_profile_description  = 'Full test of the pipeline in stub mode'
 
-    input                       = 'tests/stub/assemblysheet.csv'
+    input                       = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/assemblysheet.csv'
 
     ncbi_fcs_adaptor_skip       = false
     ncbi_fcs_adaptor_empire     = 'euk'
@@ -26,7 +26,7 @@ params {
     hic                         = 'tests/stub/hic/Dummy_hic.R{1,2}.fq.gz'
 
     synteny_skip                = false
-    synteny_xref_assemblies     = 'tests/stub/xrefsheet.csv'
+    synteny_xref_assemblies     = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/xrefsheet.csv'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus                    = 2