Update reference paths

README.md

@@ -194,7 +194,7 @@ input:
 | `docker_container_registry` | no | string | Registry containing tool Docker images, optional. Default: `ghcr.io/uclahs-cds` |
 | `base_resource_update` | optional | namespace | Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in `template.config` and below. |
 
- *Providing `intersect_regions` is required and will limit the final output to just those regions.  All regions of the reference genome could be provided as a `bed` file with all contigs, however it is HIGHLY recommended to remove `decoy` contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for `Mutect2` and will cause a very long runtime for `Strelka2`. See [Discussion here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216). For `uclahs-cds` users, a GRCh38 `bed.gz` file can be found here: `/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz`.
+ *Providing `intersect_regions` is required and will limit the final output to just those regions.  All regions of the reference genome could be provided as a `bed` file with all contigs, however it is HIGHLY recommended to remove `decoy` contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for `Mutect2` and will cause a very long runtime for `Strelka2`. See [Discussion here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216). For `uclahs-cds` users, a GRCh38 `bed.gz` file can be found here: `/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz`.
 
  ### Base resource allocation updaters
 To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the [input.config](config/template.config) file. The default allocations can be found in the [node-specific config files](./config/)
@@ -258,8 +258,8 @@ base_resource_update {
 | filter_mutect_calls_extra_args | no | string | Additional arguments for the FilterMutectCalls command |
 | gatk_command_mem_diff | yes | nextflow.util.MemoryUnit | How much to subtract from the task's allocated memory where the remainder is the Java heap max. (should not be changed unless task fails for memory related reasons) |
 | scatter_count | yes | int | Number of intervals to split the desired interval into. Mutect2 will call each interval seperately. |
-| germline_resource_gnomad_vcf | no | path | A stripped down version of the [gnomAD VCF](https://gnomad.broadinstitute.org/) stripped of all unneeded INFO fields, keeping only AF, currently available for GRCh38:`/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz` and GRCh37: `/hot/ref/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf`. |
-| panel_of_normals_vcf | no | path | VCF file of sites observed in normal. Currently available for GRCh38: `/hot/ref/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz`. This could be useful for tumor only mode. |
+| germline_resource_gnomad_vcf | no | path | A stripped down version of the [gnomAD VCF](https://gnomad.broadinstitute.org/) stripped of all unneeded INFO fields, keeping only AF, currently available for GRCh38:`/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz` and GRCh37: `/hot/resource/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf`. |
+| panel_of_normals_vcf | no | path | VCF file of sites observed in normal. Currently available for GRCh38: `/hot/resource/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz`. This could be useful for tumor only mode. |
 
 #### MuSE Specific Configuration
 | Input       | Required | Type   | Description                               |
@@ -348,7 +348,7 @@ Tumor BAM: `/hot/resource/pipeline_testing_set/WGS/GRCh38/A/full/CPCG0000000196-
 |call_sIndel_Manta        |1h 35m 25s         |1848.6% |11.7 GB        |
 |call_sSNV_Strelka2       |59m 19s        |3234.0%  |8.2 GB       |
 
-Therefore, we strongly suggest to use the `--callRegions` if the non-canonical region is unnecessary. `-callRegions`'s input `bed.gz` file can be found here: `/hot/ref/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz`. For other genome version, you can use [UCSC Liftover](https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert.
+Therefore, we strongly suggest to use the `--callRegions` if the non-canonical region is unnecessary. `-callRegions`'s input `bed.gz` file can be found here: `/hot/resource/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz`. For other genome version, you can use [UCSC Liftover](https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert.
 
 #### MuSE v2.0
 MuSE v2.0 was tested with a normal/tumor paired CPCG0196 WGS sample on a F32 slurm-dev node.

config/template.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = [] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     output_dir = ''
     dataset_id = ''
     // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2
@@ -31,10 +31,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Variant Intersection options
     ncbi_build = 'GRCh38'

input/example-test-multi-sample.yaml

@@ -3,9 +3,9 @@ patient_id: 'TWGSAMIN000001'
 # For multi samples, list the BAMs under the corresponding state (normal or tumor).
 input:
   normal:
-    - BAM: /hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
+    - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
   tumor:
-    - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
+    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
       contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table
-    - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam
+    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam
       contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n1_getpileupsummaries_calculatecontamination.table

input/example-test-tumor-only.yaml

@@ -2,5 +2,5 @@
 patient_id: 'TWGSAMIN000001'
 input:
   tumor:
-    - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
+    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
       contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n1_getpileupsummaries_calculatecontamination.table

input/example-test.yaml

@@ -3,7 +3,7 @@ patient_id: 'TWGSAMIN000001'
 # For multi samples, just list all the bams under the normal or tumor.
 input:
   normal:
-    - BAM: /hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
+    - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
   tumor:
-    - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
+    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
       contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n1_getpileupsummaries_calculatecontamination.table

test/config/a_mini-all-tools.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['somaticsniper', 'strelka2', 'mutect2', 'muse']
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
      // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE
     exome = false
@@ -29,10 +29,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'

test/config/a_mini-muse.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['muse'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
     // set params.exome to TRUE will add the '--exome' option when running manta and strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE
@@ -30,10 +30,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'

test/config/a_mini-mutect2.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['mutect2'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
     // set params.exome to TRUE will add the '--exome' option when running manta and strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE
@@ -30,10 +30,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'

test/config/a_mini-somaticsniper.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['somaticsniper'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
     // set params.exome to TRUE will add the '--exome' option when running manta and strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE
@@ -30,10 +30,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'

test/config/a_mini-strelka2.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['strelka2'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
     // set params.exome to TRUE will add the '--exome' option when running manta and strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE
@@ -30,10 +30,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'

test/config/a_mini-two-tools.config

@@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config"
 
 params {
     algorithm = ['somaticsniper', 'strelka2']
-    reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
-    intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     dataset_id = 'TWGSAMIN'
      // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE
     exome = false
@@ -29,10 +29,10 @@ params {
     filter_mutect_calls_extra_args = ''
     gatk_command_mem_diff = 500.MB
     scatter_count = 50
-    germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
 
     // MuSE options
-    dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 
     // Intersect options
     ncbi_build = 'GRCh38'