Update gitignore

.gitignore

@@ -5,6 +5,7 @@ src/__pycache__
 src/test_utils.py
 databases/*
 cromwell/*
+cromwell-executions/
 .ipynb_checkpoints
 docker/gene-mapper/tests/__pycache__/*
 tests/*

src/config.json

@@ -24,9 +24,9 @@
         "f2_generate_gene_catalog": "./input_templates/f2_generate_gene_catalog.json",
         "f3_map_to_gene_clusters": "./input_templates/f3_map_to_gene_clusters.json",
         "f4_annotate_gene_catalog": "./input_templates/f4_annotate_gene_catalog.json",
+        "generate_table": "./input_templates/generate_table.json",
         "qc_and_assembly": "./input_templates/qc_and_assembly.json",
-        "t1_predict_mags": "./input_templates/t1_predict_mags.json",
-        "generate_table" : "./input_templates/generate_table.json"
+        "t1_predict_mags": "./input_templates/t1_predict_mags.json"
     },
     "read_extensions": [
         ".fastq",
@@ -35,7 +35,7 @@
         ".fq.gz"
     ],
     "system_paths": {
-        "cromwell_path": "/storage/TomaszLab/vbez/metagenomic_gmhi/metagenomome_assembly/cromwell/cromwell-84.jar",
+        "cromwell_path": "/app/cromwell-84.jar",
         "db_mount_config": "./mount.conf",
         "output_config_path": "./input_templates/output_options.json"
     },
@@ -44,8 +44,8 @@
         "f2_generate_gene_catalog": "./wdl/f2_generate_gene_catalog.wdl",
         "f3_map_to_gene_clusters": "./wdl/f3_map_to_gene_clusters.wdl",
         "f4_annotate_gene_catalog": "./wdl/f4_annotate_gene_catalog.wdl",
+        "generate_table": "./wdl/generate_table.wdl",
         "qc_and_assembly": "./wdl/qc_and_assembly.wdl",
-        "t1_predict_mags": "./wdl/t1_predict_mags.wdl",
-        "generate_table" : "./wdl/generate_table.wdl"
+        "t1_predict_mags": "./wdl/t1_predict_mags.wdl"
     }
 }