Update for version 0.9

iwc-workflows · Oct 23, 2023 · 0559adb · 0559adb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.9] 2023-10-23
+
+Fix the normalization factor. It was coverage per reads and per reads in peaks instead of per million reads and per million reads in peaks.
+
 ## [0.8] 2023-10-19
 
 Fix the remove duplicate step!

diff --git a/atacseq.ga b/atacseq.ga
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.8",
+    "release": "0.9",
     "name": "ATACseq",
     "steps": {
         "0": {
@@ -463,7 +463,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "ddf54b12c295",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -775,7 +775,12 @@
                     "output_name": "outputcnt"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Compute",
+                    "name": "input"
+                }
+            ],
             "label": "compute 1/million reads",
             "name": "Compute",
             "outputs": [
@@ -802,7 +807,7 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.0",
             "type": "tool",
             "uuid": "ec62cddf-fb04-4185-b9f4-709de2ce0202",
@@ -954,7 +959,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "ddf54b12c295",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1267,7 +1272,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "ddf54b12c295",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1296,7 +1301,12 @@
                     "output_name": "outfile"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Compute",
+                    "name": "input"
+                }
+            ],
             "label": "compute 1/million reads in peaks",
             "name": "Compute",
             "outputs": [
@@ -1323,7 +1333,7 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.0",
             "type": "tool",
             "uuid": "5f55e258-a4fe-4b51-ab9b-2a6f0f22d910",
@@ -1445,7 +1455,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "ddf54b12c295",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1615,6 +1625,6 @@
     "tags": [
         "ATACseq"
     ],
-    "uuid": "7e9c63dd-6b70-494c-be92-cc732eaea90d",
-    "version": 2
+    "uuid": "acfc2893-ea3c-429b-900f-6926ca7f04a5",
+    "version": 1
 }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -21,7 +21,7 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "datePublished": "2023-10-19T15:11:18.072068",
+            "datePublished": "2023-10-23T15:16:21.551531",
             "hasPart": [
                 {
                     "@id": "atacseq.ga"
@@ -72,7 +72,7 @@
                 "@id": "#galaxy"
             },
             "url": "https://github.com/iwc-workflows/atacseq",
-            "version": "0.8"
+            "version": "0.9"
         },
         {
             "@id": "#galaxy",