Update for version 0.6

iwc-workflows · Oct 3, 2023 · 9c9bc6f · 9c9bc6f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.6] 2023-09-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0`
+
 ## [0.5.1] 2023-09-22
 
 Fix bug in normalize profiles when used with multiple samples (in 0.5.0 it is averaging samples instead of normalizing each sample).

diff --git a/atacseq.ga b/atacseq.ga
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.5.1",
+    "release": "0.6",
     "name": "ATACseq",
     "steps": {
         "0": {
@@ -175,7 +175,7 @@
                 "owner": "lparsons",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Nextera R2\", \"adapter2\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Nextera R2\", \"adapter2\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.4+galaxy0",
             "type": "tool",
             "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7",
@@ -242,7 +242,7 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.5.0+galaxy0",
             "type": "tool",
             "uuid": "c32a3847-f673-487f-af98-8d50999f2d21",
@@ -407,7 +407,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4",
             "tool_shed_repository": {
-                "changeset_revision": "585027e65f3b",
+                "changeset_revision": "f9242e01365a",
                 "name": "picard",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -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": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -520,7 +520,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"ed_score\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"split\": false, \"tag\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"ed_score\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"split\": false, \"tag\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.30.0+galaxy2",
             "type": "tool",
             "uuid": "12ca18f2-222b-4e9c-8ae0-b5772cd51bd7",
@@ -954,7 +954,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1085,7 +1085,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0",
             "tool_shed_repository": {
-                "changeset_revision": "fe5b4cb8356c",
+                "changeset_revision": "a68aa6c1204a",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1105,7 +1105,7 @@
         },
         "21": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0",
             "errors": null,
             "id": 21,
             "input_connections": {
@@ -1149,15 +1149,15 @@
                     "output_name": "outFileName"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "f6f246438eda",
+                "changeset_revision": "4a53856a5b85",
                 "name": "deeptools_bigwig_average",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"skipNAs\": false, \"scaleFactors\": {\"__class__\": \"ConnectedValue\"}, \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bigwigs\": {\"__class__\": \"ConnectedValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "3.5.2+galaxy0",
+            "tool_version": "3.5.4+galaxy0",
             "type": "tool",
             "uuid": "fa2633cf-af38-43eb-8c9f-b8b656d6a631",
             "when": null,
@@ -1267,7 +1267,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1445,7 +1445,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1459,7 +1459,7 @@
         },
         "28": {
             "annotation": "Isolate each bigwig do normalize not average",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0",
             "errors": null,
             "id": 28,
             "input_connections": {
@@ -1503,15 +1503,15 @@
                     "output_name": "outFileName"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "f6f246438eda",
+                "changeset_revision": "4a53856a5b85",
                 "name": "deeptools_bigwig_average",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"skipNAs\": false, \"scaleFactors\": {\"__class__\": \"ConnectedValue\"}, \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bigwigs\": {\"__class__\": \"ConnectedValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "3.5.2+galaxy0",
+            "tool_version": "3.5.4+galaxy0",
             "type": "tool",
             "uuid": "8eab7f49-605b-462a-9806-da0c795117f3",
             "when": null,

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -21,7 +21,7 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "datePublished": "2023-09-25T12:10:50.925708",
+            "datePublished": "2023-10-03T10:13:49.682562",
             "hasPart": [
                 {
                     "@id": "atacseq.ga"
@@ -72,7 +72,7 @@
                 "@id": "#galaxy"
             },
             "url": "https://github.com/iwc-workflows/atacseq",
-            "version": "0.5.1"
+            "version": "0.6"
         },
         {
             "@id": "#galaxy",