From dd141681a10530c1bf315e4d64b6d85c424d5017 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 6 Jul 2026 10:56:28 +0000 Subject: [PATCH] Updating workflows/variant-calling/ploidy-aware-genotype-calling from 0.1.2 to 0.1.3 --- .../CHANGELOG.md | 7 +++++ .../genotype-variant-calling-wgs-pe.ga | 30 +++++++++---------- 2 files changed, 22 insertions(+), 15 deletions(-) diff --git a/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md b/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md index d23612cd25..d5f20f6adf 100644 --- a/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md +++ b/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.1.3] - 2026-07-06 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.6+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1` + ## [0.1.2] - 2026-04-20 ### Automatic update diff --git a/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga b/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga index f60ccb0ee2..93f046a4d8 100644 --- a/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga +++ b/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga @@ -202,7 +202,7 @@ }, "4": { "annotation": "Processing of FASTQ files", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.6+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -244,16 +244,16 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.6+galaxy0", "tool_shed_repository": { - "changeset_revision": "241decaaff3e", + "changeset_revision": "68386e630362", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"duplicated_reads\": {\"handling_options\": {\"eval_dups\": \"--dont_eval_duplication\", \"__current_case__\": 0}}, \"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_front_select\": {\"cut_front\": \"\", \"__current_case__\": 1}, \"cut_tail_select\": {\"cut_tail\": \"\", \"__current_case__\": 1}, \"cut_right_select\": {\"cut_right\": \"\", \"__current_case__\": 1}}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__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__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.3.2+galaxy0", + "tool_version": "1.3.6+galaxy0", "type": "tool", "uuid": "e1359474-a019-4a41-963b-ff2660bd36cc", "when": null, @@ -316,7 +316,7 @@ }, "6": { "annotation": "Mapping reads with reference sequence", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -352,16 +352,16 @@ "top": 130.88609138292358 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1", "tool_shed_repository": { - "changeset_revision": "1dfc975b48d5", + "changeset_revision": "c598cbb8b019", "name": "bwa", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": null}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.7.19", + "tool_version": "0.7.19+galaxy1", "type": "tool", "uuid": "fe62b57d-20f0-40db-a4f3-6b801a66e9a3", "when": null, @@ -501,7 +501,7 @@ }, "10": { "annotation": "Aggregation of results from mapping, and other preprocessing steps", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", "errors": null, "id": 10, "input_connections": { @@ -554,16 +554,16 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", "tool_shed_repository": { - "changeset_revision": "862943c10425", + "changeset_revision": "fac2260bc88a", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 8, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 25, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 18, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.33+galaxy3", + "tool_version": "1.35+galaxy1", "type": "tool", "uuid": "6543abd4-0be4-4027-90e5-57644220bba3", "when": null, @@ -670,7 +670,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.22+galaxy0", "tool_shed_repository": { - "changeset_revision": "5fa262ce95dd", + "changeset_revision": "5226c31ac6d3", "name": "bcftools_norm", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -863,7 +863,7 @@ "Diploid", "FreeBayes" ], - "uuid": "dceed42d-a43a-485e-9f36-fc96628433ec", + "uuid": "07890262-3a6d-4d9f-8e71-6df52d474db2", "version": 1, - "release": "0.1.2" + "release": "0.1.3" } \ No newline at end of file