xengsort_idx_name correction to GRCm39

TheJacksonLaboratory · May 7, 2024 · d52cb0b · d52cb0b
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Showing 12 changed files with 12 additions and 12 deletions.
diff --git a/.gitignore b/.gitignore
@@ -13,4 +13,4 @@ test.csv
 test2.csv
 .nf-test
 .nf-test.log
-nf-test-report.tap
+nf-test-report*
diff --git a/bin/help/pta.nf b/bin/help/pta.nf
@@ -15,7 +15,7 @@ The following are human specific parameters. To see help for mouse, add `--gen_o
 --pdx | false | Options: false, true. If specified, 'Xengsort' is run on reads to deconvolute human and mouse reads. Human only reads are used in analysis. 
 --xengsort_host_fasta | '/projects/compsci/omics_share/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa' | Xengsort host fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_idx_path | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xengsort' | Xengsort index for deconvolution of human and mouse reads. Used when `--pdx` is run. If `null`, Xengsort Index is run using ref_fa and host_fa.  
---xengsort_idx_name | 'hg38_GRCm38-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
+--xengsort_idx_name | 'hg38_GRCm39-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
 
 --deduplicate_reads | false | Options: false, true. If specified, run bbmap clumpify on input reads. Clumpify will deduplicate reads prior to trimming. This can help with mapping and downstream steps when analyzing high coverage WGS data. 
 

diff --git a/bin/help/rna_fusion.nf b/bin/help/rna_fusion.nf
@@ -50,7 +50,7 @@ Parameter | Default | Description
 --ref_fa | '/projects/compsci/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'| Xengsort graft fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_host_fasta | '/projects/compsci/omics_share/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa' | Xengsort host fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_idx_path | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xengsort' | Xengsort index for deconvolution of human and mouse reads. Used when `--pdx` is run. If `null`, Xengsort Index is run using ref_fa and host_fa.  
---xengsort_idx_name | 'hg38_GRCm38-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
+--xengsort_idx_name | 'hg38_GRCm39-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
 
 '''
 }

diff --git a/bin/help/rnaseq.nf b/bin/help/rnaseq.nf
@@ -52,7 +52,7 @@ Parameter | Default | Description
 --ref_fa | '/projects/compsci/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'| Xengsort graft fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_host_fasta | '/projects/compsci/omics_share/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa' | Xengsort host fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_idx_path | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xengsort' | Xengsort index for deconvolution of human and mouse reads. Used when `--pdx` is run. If `null`, Xengsort Index is run using ref_fa and host_fa.  
---xengsort_idx_name | 'hg38_GRCm38-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
+--xengsort_idx_name | 'hg38_GRCm39-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
 
 
 There are two additional parameters that are human specific. They are: 

diff --git a/bin/help/somatic_wes.nf b/bin/help/somatic_wes.nf
@@ -24,7 +24,7 @@ Parameter | Default | Description
 --pdx | false | Options: false, true. If specified, 'Xengsort' is run on reads to deconvolute human and mouse reads. Human only reads are used in analysis. 
 --xengsort_host_fasta | '/projects/compsci/omics_share/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa' | Xengsort host fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_idx_path = | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xengsort' | Xengsort index for deconvolution of human and mouse reads. Used when `--pdx` is run. If `null`, Xengsort Index is run using ref_fa and host_fa.  
---xengsort_idx_name = | 'hg38_GRCm38-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
+--xengsort_idx_name = | 'hg38_GRCm39-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
 
 --genotype_targets | '/projects/compsci/omics_share/human/GRCh38/supporting_files/ancestry_panel/snp_panel_v2_targets_annotations.snpwt.bed.gz' | Target SNP bed file for the ancestry panel. Can contain annotation information. 
 --snpID_list | '/projects/compsci/omics_share/human/GRCh38/supporting_files/ancestry_panel/snp_panel_v2.list' | Target SNPs in list used in BCFtools filtering step

diff --git a/bin/help/somatic_wes_pta.nf b/bin/help/somatic_wes_pta.nf
@@ -24,7 +24,7 @@ Parameter | Default | Description
 --pdx | false | Options: false, true. If specified, 'Xengsort' is run on reads to deconvolute human and mouse reads. Human only reads are used in analysis. 
 --xengsort_host_fasta | '/projects/compsci/omics_share/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa' | Xengsort host fasta file. Used by Xengsort Index when `--pdx` is run, and xengsort_idx_path is `null` or false.  
 --xengsort_idx_path = | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xengsort' | Xengsort index for deconvolution of human and mouse reads. Used when `--pdx` is run. If `null`, Xengsort Index is run using ref_fa and host_fa.  
---xengsort_idx_name = | 'hg38_GRCm38-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
+--xengsort_idx_name = | 'hg38_GRCm39-NOD_ShiLtJ' | Xengsort index name associated with files located in `xengsort_idx_path` or name given to outputs produced by Xengsort Index
 
 --genotype_targets | '/projects/compsci/omics_share/human/GRCh38/supporting_files/ancestry_panel/snp_panel_v2_targets_annotations.snpwt.bed.gz' | Target SNP bed file for the ancestry panel. Can contain annotation information. 
 --snpID_list | '/projects/compsci/omics_share/human/GRCh38/supporting_files/ancestry_panel/snp_panel_v2.list' | Target SNPs in list used in BCFtools filtering step

diff --git a/config/pta.config b/config/pta.config
@@ -32,7 +32,7 @@ params {
     // xengsort index  
     xengsort_host_fasta = params.reference_cache+'/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa'
     xengsort_idx_path = params.reference_cache+'/human/GRCh38/supporting_files/xengsort'
-    xengsort_idx_name = 'hg38_GRCm38-NOD_ShiLtJ'
+    xengsort_idx_name = 'hg38_GRCm39-NOD_ShiLtJ'
 
     // Reference fasta
     ref_fa = params.reference_cache+'/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'

diff --git a/config/rna_fusion.config b/config/rna_fusion.config
@@ -25,7 +25,7 @@ params {
   ref_fa = params.reference_cache+'/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'
   xengsort_host_fasta = params.reference_cache+'/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa'
   xengsort_idx_path = params.reference_cache+'/human/GRCh38/supporting_files/xengsort'
-  xengsort_idx_name = 'hg38_GRCm38-NOD_ShiLtJ'
+  xengsort_idx_name = 'hg38_GRCm39-NOD_ShiLtJ'
 
   // READ LENGTH ADJUSTMENTS: 
   read_length = 150 // change relative to sample being processed. 75, 100, 125, and 150 are supported. 

diff --git a/config/rnaseq.config b/config/rnaseq.config
@@ -109,7 +109,7 @@ if (params.gen_org=='human' && params.pdx){
     params.ref_fa = params.reference_cache+'/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'
     params.xengsort_host_fasta = params.reference_cache+'/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa'
     params.xengsort_idx_path = params.reference_cache+'/human/GRCh38/supporting_files/xengsort'
-    params.xengsort_idx_name = 'hg38_GRCm38-NOD_ShiLtJ'
+    params.xengsort_idx_name = 'hg38_GRCm39-NOD_ShiLtJ'
 
     // General RSEM 
     params.seed_length = '25'

diff --git a/config/somatic_wes.config b/config/somatic_wes.config
@@ -43,7 +43,7 @@ params {
   // Xengsort index
   xengsort_host_fasta = params.reference_cache+'/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa'
   xengsort_idx_path = params.reference_cache+'/human/GRCh38/supporting_files/xengsort'
-  xengsort_idx_name = 'hg38_GRCm38-NOD_ShiLtJ'
+  xengsort_idx_name = 'hg38_GRCm39-NOD_ShiLtJ'
 
   // WES capture array BED and GATK intervals lists
   target_gatk = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.bed'

diff --git a/config/somatic_wes_pta.config b/config/somatic_wes_pta.config
@@ -40,7 +40,7 @@ params {
   // include for Xengsort index
   xengsort_host_fasta = params.reference_cache+'/mouse/GRCm39/genome/sequence/imputed/rel_2112_v8/NOD_ShiLtJ.39.fa'
   xengsort_idx_path = params.reference_cache+'/human/GRCh38/supporting_files/xengsort'
-  xengsort_idx_name = 'hg38_GRCm38-NOD_ShiLtJ'
+  xengsort_idx_name = 'hg38_GRCm39-NOD_ShiLtJ'
 
   // WES capture array BED and GATK intervals lists
   target_gatk = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.bed'

diff --git a/tests/workflows/rnaseq.nf.test b/tests/workflows/rnaseq.nf.test
@@ -69,7 +69,7 @@ nextflow_workflow {
             params {
                 outdir = "tests/results"
                 gen_org = "human"
-                sample_folder = "${baseDir}/test/rna/human"
+                sample_folder = "${baseDir}/test/rna/human/pdx"
                 pubdir = "tests/results"
                 pdx = true
                 pipeline = 'rnaseq'