diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/.gitmodules b/.gitmodules old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml old mode 100644 new mode 100755 diff --git a/docs/.keep b/docs/.keep old mode 100644 new mode 100755 diff --git a/docs/index.md b/docs/index.md old mode 100644 new mode 100755 index 81bd63d24292a57ccbced426262c866175fb8c9e..8f47c0ec35fb5331965905763e599314d9aa654d --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ # ATAC-seq Astrocyte Workflow -<!-- TODO: Fill out intro (AS) --> +ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis. It is built upon ENCODE ATAC workflow written in workflow description language and uses Nextflow to run in the astrocyte platform. ## Requirements - The ATAC-seq Source workflow ['astrocyte-atac-source] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-source). diff --git a/test_data/.keep b/test_data/.keep old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/ENCSR356KRQ_subsampled.json b/test_data/example_input_json/ENCSR356KRQ_subsampled.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/ENCSR356KRQ_subsampled_dx.json b/test_data/example_input_json/dx/ENCSR356KRQ_subsampled_dx.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/ENCSR356KRQ_subsampled_rep1_dx.json b/test_data/example_input_json/dx/ENCSR356KRQ_subsampled_rep1_dx.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/template_general.json b/test_data/example_input_json/dx/template_general.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/template_hg19.json b/test_data/example_input_json/dx/template_hg19.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/template_hg38.json b/test_data/example_input_json/dx/template_hg38.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/template_mm10.json b/test_data/example_input_json/dx/template_mm10.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx/template_mm9.json b/test_data/example_input_json/dx/template_mm9.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/ENCSR356KRQ_subsampled_dx_azure.json b/test_data/example_input_json/dx_azure/ENCSR356KRQ_subsampled_dx_azure.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/template_general.json b/test_data/example_input_json/dx_azure/template_general.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/template_hg19.json b/test_data/example_input_json/dx_azure/template_hg19.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/template_hg38.json b/test_data/example_input_json/dx_azure/template_hg38.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/template_mm10.json b/test_data/example_input_json/dx_azure/template_mm10.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/dx_azure/template_mm9.json b/test_data/example_input_json/dx_azure/template_mm9.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/template.full.json b/test_data/example_input_json/template.full.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/template.json b/test_data/example_input_json/template.json old mode 100644 new mode 100755 diff --git a/test_data/example_input_json/terra/ENCSR356KRQ_subsampled.terra.json b/test_data/example_input_json/terra/ENCSR356KRQ_subsampled.terra.json old mode 100644 new mode 100755 diff --git a/vizapp/.keep b/vizapp/.keep old mode 100644 new mode 100755 diff --git a/workflow/configs/biohpc.config b/workflow/configs/biohpc.config old mode 100644 new mode 100755 diff --git a/workflow/images/singularity/.keep b/workflow/images/singularity/.keep old mode 100644 new mode 100755 diff --git a/workflow/main.nf b/workflow/main.nf old mode 100644 new mode 100755 diff --git a/workflow/scripts/.keep b/workflow/scripts/.keep old mode 100644 new mode 100755