diff --git a/workflows/epigenetics/atacseq/CHANGELOG.md b/workflows/epigenetics/atacseq/CHANGELOG.md index c6d48234f..eaac18e1f 100644 --- a/workflows/epigenetics/atacseq/CHANGELOG.md +++ b/workflows/epigenetics/atacseq/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [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). + ## [0.5] 2023-03-17 ### Automatic update diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/workflows/epigenetics/atacseq/atacseq.ga index 0e731852c..55046e235 100644 --- a/workflows/epigenetics/atacseq/atacseq.ga +++ b/workflows/epigenetics/atacseq/atacseq.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.5", + "release": "0.5.1", "name": "ATACseq", "steps": { "0": { @@ -175,7 +175,7 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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_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_version": "4.4+galaxy0", "type": "tool", "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7", @@ -418,15 +418,15 @@ "uuid": "d0a9998c-18a9-4579-8d33-f0897e1ceaeb", "when": null, "workflow_outputs": [ - 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"id": 22, + "id": 23, "input_connections": { "infile": { - "id": 21, + "id": 22, "output_name": "output" } }, @@ -1246,14 +1285,14 @@ } ] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "input": { - "id": 22, + "id": 23, "output_name": "outfile" } }, @@ -1267,8 +1306,8 @@ } ], "position": { - "left": 1884.0994594973222, - "top": 1705.217377312037 + "left": 1660.7476485833522, + "top": 1675.7739064754614 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -1291,14 +1330,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "25": { "annotation": "", "content_id": "cat1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input1": { - "id": 22, + "id": 23, "output_name": "outfile" }, "queries_0|input2": { @@ -1334,14 +1373,14 @@ "when": null, "workflow_outputs": [] }, - "25": { + "26": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - 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