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ameyner2 · mwham · mwham · mwham · mwham · mwham
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+---
+
+image: trio-whole-exome:v1
+
 test:
  script:
-  - conda env create -p $PWD/conda
-  - conda activate $PWD/conda
-  - cd tests/ && ./run_tests.sh
-  - conda deactivate
+  - cd tests/ && ./run_stubs.sh
--- a/trio_whole_exome_bcbio_template.yaml
+++ b/trio_whole_exome_bcbio_template.yaml
@@ -19,4 +19,5 @@ details:
  analysis: variant2
  genome_build: hg38
 upload:
-  dir: /home/u035/u035/shared/results
+  # relative path will output locally to the bcbio run folder
+  dir: ./results 
--- a/G2P.pm
+++ b/G2P.pm
--- a/NHS_WES_check_PED_aff_probands.py
+++ b/NHS_WES_check_PED_aff_probands.py
--- a/NHS_WES_check_PED_quad.py
+++ b/NHS_WES_check_PED_quad.py
--- a/NHS_WES_extract_shared_vars.py
+++ b/NHS_WES_extract_shared_vars.py
--- a/NHS_WES_extract_trio_FAM_PRO_ID.py
+++ b/NHS_WES_extract_trio_FAM_PRO_ID.py
--- a/NHS_WES_filter_LQ_GT.py
+++ b/NHS_WES_filter_LQ_GT.py
--- a/NHS_WES_generate_DEC_IGV.py
+++ b/NHS_WES_generate_DEC_IGV.py
--- a/NHS_WES_generate_DEC_IGV.py.v1
+++ b/NHS_WES_generate_DEC_IGV.py.v1
--- a/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
+++ b/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
--- a/NHS_WES_generate_DEC_IGV_aff_probands.py
+++ b/NHS_WES_generate_DEC_IGV_aff_probands.py
--- a/NHS_WES_generate_DEC_IGV_sib_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
--- a/NHS_WES_generate_DEC_IGV_trio_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_trio_from_quad.py
--- a/NHS_WES_generate_aff_sib_ped.py
+++ b/NHS_WES_generate_aff_sib_ped.py
--- a/NHS_WES_generate_coverage_result_file.py
+++ b/NHS_WES_generate_coverage_result_file.py
--- a/NHS_WES_generate_trio_VCF.py
+++ b/NHS_WES_generate_trio_VCF.py
--- a/NHS_WES_generate_trio_ped.py
+++ b/NHS_WES_generate_trio_ped.py
--- a/NHS_WES_trio_cram_setup.sh
+++ b/NHS_WES_trio_cram_setup.sh
--- a/NHS_WES_trio_delete_BAM.sh
+++ b/NHS_WES_trio_delete_BAM.sh
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