Updating workflows/genome-assembly/quality-and-contamination-control from 1.1.6 to 1.1.7

Author: planemo-autoupdate

workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [1.1.7] 2025-03-17
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4`
+- `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.1+galaxy0`
+
 ## [1.1.6] - 2024-11-18
 
 ### Automatic update

workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga

@@ -27,7 +27,7 @@
     ],
     "format-version": "0.1",
     "license": "GPL-3.0-or-later",
-    "release": "1.1.6",
+    "release": "1.1.7",
     "name": "Quality and Contamination Control For Genome Assembly",
     "steps": {
         "0": {
@@ -104,7 +104,7 @@
                 "top": 307.433349609375
             },
             "tool_id": null,
-            "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "1a56b57e-8893-4cbc-a984-329e0b815cbd",
@@ -137,7 +137,7 @@
                 "top": 454.91066885428484
             },
             "tool_id": null,
-            "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "daac0634-bcf4-4fdd-bcd2-67247f5afdd0",
@@ -152,24 +152,16 @@
         },
         "4": {
             "annotation": "fastp_triming, quality analaysis and read cleaning",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4",
             "errors": null,
             "id": 4,
             "input_connections": {
                 "single_paired|in1": {
                     "id": 0,
                     "output_name": "output"
-                },
-                "single_paired|in2": {
-                    "id": 1,
-                    "output_name": "output"
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool fastp",
-                    "name": "single_paired"
-                },
                 {
                     "description": "runtime parameter for tool fastp",
                     "name": "single_paired"
@@ -182,10 +174,6 @@
                     "name": "out1",
                     "type": "input"
                 },
-                {
-                    "name": "out2",
-                    "type": "input"
-                },
                 {
                     "name": "report_html",
                     "type": "html"
@@ -271,15 +259,15 @@
                     "output_name": "report_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4",
             "tool_shed_repository": {
-                "changeset_revision": "a626e8c0e1ba",
+                "changeset_revision": "10678d49d39e",
                 "name": "fastp",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.24.0+galaxy3",
+            "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"RuntimeValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.24.0+galaxy4",
             "type": "tool",
             "uuid": "7f405009-2491-4633-b4e1-ca0fdbd8360d",
             "when": null,
@@ -319,10 +307,6 @@
                 "single_paired|forward_input": {
                     "id": 4,
                     "output_name": "out1"
-                },
-                "single_paired|reverse_input": {
-                    "id": 4,
-                    "output_name": "out2"
                 }
             },
             "inputs": [
@@ -408,7 +392,7 @@
         },
         "6": {
             "annotation": "bracken_abundance_estimation",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -468,15 +452,15 @@
                     "output_name": "report"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "0c7b6eb7e752",
+                "changeset_revision": "4d350ac5148e",
                 "name": "bracken",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": {\"__class__\": \"ConnectedValue\"}, \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "3.0+galaxy0",
+            "tool_version": "3.1+galaxy0",
             "type": "tool",
             "uuid": "e088cdc6-d79b-453c-8787-6d4b7004312a",
             "when": null,
@@ -495,7 +479,7 @@
         },
         "7": {
             "annotation": "recentrifuge_taxonomy_visualization",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.1+galaxy0",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -596,15 +580,15 @@
                     "output_name": "stat_tsv"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "591175c0f051",
+                "changeset_revision": "612df2a5054f",
                 "name": "recentrifuge",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": {\"__class__\": \"ConnectedValue\"}}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.15.0+galaxy0",
+            "tool_version": "1.15.1+galaxy0",
             "type": "tool",
             "uuid": "2db5d20e-62c7-43ad-b21f-e9992c77faa1",
             "when": null,
@@ -649,10 +633,6 @@
                     "id": 4,
                     "output_name": "out1"
                 },
-                "tool_section|tools_0|select_tool|trimmed_reverse_R2_path": {
-                    "id": 4,
-                    "output_name": "out2"
-                },
                 "tool_section|tools_1|select_tool|input": {
                     "id": 5,
                     "output_name": "report_output"