updates to support new chr14 chr16 test data

mskcc · May 1, 2018 · 5d5bbd4 · 5d5bbd4
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commit 5d5bbd4
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Showing 6 changed files with 6 additions and 223 deletions.
diff --git a/README.md b/README.md
@@ -94,11 +94,6 @@ To run with Toil batch system runner:
 ```
 (innovation_pipeline) ~/PIPELINE_RUNS$ toil-cwl-runner  ~/Innovation-Pipeline/workflows/innovation_pipeline.cwl runs/inputs_pipeline_test.yaml
 ```
-or use:
-```
-(innovation_pipeline) ~/PIPELINE_RUNS$ test/run-pipeline-test.sh ~/output_dir
-```
-Have a look inside `pipeline_runner.sh` to see some useful arguments for Toil & cwltool
 
 # Running a real run
 The same steps for testing can be used for a real run.

diff --git a/pipeline-runner.sh b/pipeline-runner.sh
diff --git a/resources/run_files/test.yaml b/resources/run_files/test.yaml
@@ -4,15 +4,15 @@
 
 # Used in multiple steps
 # Todo: implement smaller reference fasta for testing
-reference_fasta: $PIPELINE_ROOT/test/test_data/test_reference/fasta/chr14_chr16/chr14_chr16.fasta
-reference_fasta_fai: $PIPELINE_ROOT/test/test_data/test_reference/fasta/chr14_chr16/chr14_chr16.fasta.fai
+reference_fasta: /home/johnsoni/test_reference/fasta/chr14_chr16.fasta
+reference_fasta_fai: /home/johnsoni/test_reference/fasta/chr14_chr16.fasta.fai
 #reference_fasta: /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta
 #reference_fasta_fai: /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta.fai
 
 
 # BaseRecalibrator
 # Todo: Consolidate
-bqsr__knownSites_dbSNP: {class: File, path: $PIPELINE_ROOT/test/test_data/test_reference/vcf/chr14_chr16/dbsnp_137_14_16.b37.vcf}
-bqsr__knownSites_millis: {class: File, path: $PIPELINE_ROOT/test/test_data/test_reference/vcf/chr14_chr16/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf}
+bqsr__knownSites_dbSNP: {class: File, path: /home/johnsoni/test_reference/vcf/dbsnp_137_14_16.b37.vcf}
+bqsr__knownSites_millis: {class: File, path: /home/johnsoni/test_reference/vcf/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf}
 #bqsr__knownSites_dbSNP: {class: File, path: /ifs/e63data/bergerm1/Resources/DMP/pubdata/dbSNP/VERSIONS/dbsnp_v137/dbsnp_137.b37.vcf}
 #bqsr__knownSites_millis: {class: File, path: /ifs/e63data/bergerm1/Resources/DMP/pubdata/mills-and-1000g/VERSIONS/v20131014/Mills_and_1000G_gold_standard.indels.b37.vcf}
diff --git a/resources/run_files/test__collapsing.yaml b/resources/run_files/test__collapsing.yaml
@@ -1,3 +1,3 @@
 # Files used in collapsing steps
-bed_file: {class: File, path: $PIPELINE_ROOT/test/test_data/test_reference/bed/pan-cancer-panel.sorted.bed}
-gene_list: {class: File, path: $PIPELINE_ROOT/test/test_data/test_reference/bed/juber-hg19-gene-list.bed}
+bed_file: {class: File, path: /home/johnsoni/test_reference/bed/pan-cancer-panel.sorted.bed}
+gene_list: {class: File, path: /home/johnsoni/test_reference/bed/juber-hg19-gene-list.bed}
diff --git a/test/inputs.yaml b/test/inputs.yaml
diff --git a/test/run-pipeline-test.sh b/test/run-pipeline-test.sh