From 7758fde7a41f6c15c90e3ef0b5ec8fc6e8009fab Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 20 Apr 2026 09:15:42 +0000 Subject: [PATCH] Updating workflows/variant-calling/ploidy-aware-genotype-calling from 0.1.1 to 0.1.2 --- .../CHANGELOG.md | 11 +++ .../genotype-variant-calling-wgs-pe.ga | 84 ++++++++----------- 2 files changed, 48 insertions(+), 47 deletions(-) diff --git a/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md b/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md index f36e47d696..d23612cd25 100644 --- a/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md +++ b/workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.1.2] - 2026-04-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0` + ## [0.1.1] 2026-03-12 - Rename workflow file to remove '+' character from filename. 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 93d18df394..f60ccb0ee2 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 @@ -50,10 +50,10 @@ { "child_steps": [ 4, - 8, 7, 10, 6, + 8, 9 ], "color": "blue", @@ -86,7 +86,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1.1", "name": "Paired end variant and ploidy-aware genotype calling", "readme": "This workflow performs end-to-end germline variant and genotype calling on paired-end Illumina sequencing data from organisms of any given ploidy. Starting from raw FASTQ reads, the workflow handles quality control, read mapping, duplicate removal, variant and genotype calling with FreeBayes, and functional annotation of the resulting variants.", "report": { @@ -203,7 +202,7 @@ }, "4": { "annotation": "Processing of FASTQ files", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -245,16 +244,16 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "ff33957bf802", + "changeset_revision": "241decaaff3e", "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": "1.1.0+galaxy0", + "tool_version": "1.3.2+galaxy0", "type": "tool", "uuid": "e1359474-a019-4a41-963b-ff2660bd36cc", "when": null, @@ -268,7 +267,7 @@ }, "5": { "annotation": "Build SnpEff database from the given reference fasta file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0", "errors": null, "id": 5, "input_connections": { @@ -300,16 +299,16 @@ "top": 828.7082651499238 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "3aae4f16ac9e", + "changeset_revision": "908f2c5fedec", "name": "snpeff", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"codon_table\": \"Standard\", \"genome_version\": \"snpeff_db\", \"input_type\": {\"input_type_selector\": \"gtf\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "5.2+galaxy1", + "tool_version": "5.4+galaxy0", "type": "tool", "uuid": "b717154e-57de-4980-ba7a-0fdd88765ff9", "when": null, @@ -370,7 +369,7 @@ }, "7": { "annotation": "Retains alignments if read is paired and mapped in proper orientation ", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2", "errors": null, "id": 7, "input_connections": { @@ -401,16 +400,16 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2", "tool_shed_repository": { - "changeset_revision": "5ec526530725", + "changeset_revision": "5cf9fcc93508", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.22+galaxy1", + "tool_version": "1.22+galaxy2", "type": "tool", "uuid": "49a309e1-22a6-455a-9fb3-77aa3f5decf4", "when": null, @@ -418,7 +417,7 @@ }, "8": { "annotation": "Generates statistics of BAM file", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9", "errors": null, "id": 8, "input_connections": { @@ -441,16 +440,16 @@ "top": 133.89804204944727 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9", "tool_shed_repository": { - "changeset_revision": "57934e90e27c", + "changeset_revision": "8fca6e1eac98", "name": "samtools_stats", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": null, \"most_inserts\": null, \"read_group\": null, \"read_length\": null, \"remove_dups\": false, \"remove_overlaps\": false, \"sparse\": false, \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.0.8", + "tool_version": "2.0.9", "type": "tool", "uuid": "a0216ddc-23e6-40e3-9088-f3934da46aa1", "when": null, @@ -502,7 +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+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", "errors": null, "id": 10, "input_connections": { @@ -555,16 +554,16 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3", "tool_shed_repository": { - "changeset_revision": "26ee5e11ecbe", + "changeset_revision": "862943c10425", "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__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "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+galaxy0", + "tool_version": "1.33+galaxy3", "type": "tool", "uuid": "6543abd4-0be4-4027-90e5-57644220bba3", "when": null, @@ -686,7 +685,7 @@ }, "13": { "annotation": "Annotates detected variants", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0", "errors": null, "id": 13, "input_connections": { @@ -738,16 +737,16 @@ "output_name": "snpeff_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "3aae4f16ac9e", + "changeset_revision": "908f2c5fedec", "name": "snpeff", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": null, \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-intron\", \"-no-utr\", \"-no-upstream\"], \"generate_gene_stats\": false, \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"outputFormat\": \"vcf\", \"snpDb\": {\"genomeSrc\": \"custom\", \"__current_case__\": 3, \"snpeff_db\": {\"__class__\": \"ConnectedValue\"}, \"codon_table\": \"Standard\"}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": \"2\", \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "5.2+galaxy1", + "tool_version": "5.4+galaxy0", "type": "tool", "uuid": "74fc9ad6-3c2c-410d-9795-540d2ae7ba6d", "when": null, @@ -766,7 +765,7 @@ }, "14": { "annotation": "Extracts required fields from the VCF file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -775,12 +774,7 @@ "output_name": "snpeff_output" } }, - "inputs": [ - { - "description": "runtime parameter for tool SnpSift Extract Fields", - "name": "input" - } - ], + "inputs": [], "label": "Extract using SnpSift", "name": "SnpSift Extract Fields", "outputs": [ @@ -794,16 +788,16 @@ "top": 644.9675784543903 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0", "tool_shed_repository": { - "changeset_revision": "5fab4f81391d", + "changeset_revision": "0abc5513f795", "name": "snpsift", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF RO AO SRP SAP EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"one_effect_per_line\": true, \"separator\": \",\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF RO AO SRP SAP EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": true, \"separator\": \",\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "4.3+t.galaxy0", + "tool_version": "5.4.0c+galaxy0", "type": "tool", "uuid": "af27808a-495d-4397-b248-6eb6c5954ce6", "when": null, @@ -820,12 +814,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Collapse Collection", - "name": "input_list" - } - ], + "inputs": [], "label": "Collapse", "name": "Collapse Collection", "outputs": [ @@ -854,7 +843,7 @@ "owner": "nml", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"RuntimeValue\"}, \"one_header\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "5.1.0", "type": "tool", @@ -874,6 +863,7 @@ "Diploid", "FreeBayes" ], - "uuid": "0706c30f-3bfb-42d5-bc55-a50d24824101", - "version": 1 + "uuid": "dceed42d-a43a-485e-9f36-fc96628433ec", + "version": 1, + "release": "0.1.2" } \ No newline at end of file