From e6a64e3e12c976daab2164e08ccb54d5ecc38381 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 15 Jul 2024 04:21:33 +0000 Subject: [PATCH 1/2] Updating workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5 from 0.1.6 to 0.1.7 --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 113 ++++++++++++++---- .../CHANGELOG.md | 6 + 2 files changed, 93 insertions(+), 26 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index d39cda8a9..1bdd01d79 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.6", + "release": "0.1.7", "name": "Assembly-Hifi-Trio-phasing-VGP5", "steps": { "0": { @@ -425,7 +425,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -434,7 +434,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -476,15 +481,15 @@ "output_name": "out1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", "tool_shed_repository": { - "changeset_revision": "fe74900d6dc7", + "changeset_revision": "aa784cb3810d", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": \"1\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}]}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"json_stats\", \"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.8+galaxy1", + "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": \"1\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}]}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"json_stats\", \"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "4.9+galaxy0", "type": "tool", "uuid": "b8770ddb-2ec4-4ef5-8362-6531e559554d", "when": null, @@ -894,7 +899,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, "id": 25, "input_connections": { @@ -923,7 +928,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -1000,15 +1018,15 @@ "output_name": "raw_unitigs_trio" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "tool_shed_repository": { - "changeset_revision": "df25d4fb79b7", + "changeset_revision": "284a1cb82b61", "name": "hifiasm", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"trio\", \"__current_case__\": 1, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"trioinput\": {\"trio_input_selector\": \"reads\", \"__current_case__\": 0, \"hap1_reads\": {\"__class__\": \"ConnectedValue\"}, \"hap2_reads\": {\"__class__\": \"ConnectedValue\"}}, \"max_kmers\": \"2\", \"min_kmers\": \"5\", \"yak_kmer_length\": \"31\", \"trio_dual\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.19.8+galaxy1", + "tool_version": "0.19.9+galaxy0", "type": "tool", "uuid": "50aee4e7-5172-49a0-a448-4020942301af", "when": null, @@ -1083,7 +1101,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1147,7 +1170,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1258,7 +1286,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1336,7 +1369,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1610,7 +1648,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1721,7 +1764,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1844,7 +1892,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2339,8 +2400,8 @@ ] } }, - "tags": "", - "uuid": "9b5cbd11-d6ce-4b59-88db-7f8597fbd891" + "tags": [], + "uuid": "1abf44d1-5ea3-43e4-bf79-76886610409b" }, "tool_id": null, "type": "subworkflow", @@ -2721,8 +2782,8 @@ ] } }, - "tags": "", - "uuid": "df2f5a94-7782-4fe9-889d-3fde55b82557" + "tags": [], + "uuid": "0e187696-f8bc-4139-96c3-3d96a5e67e51" }, "tool_id": null, "type": "subworkflow", @@ -3343,8 +3404,8 @@ ] } }, - "tags": "", - "uuid": "4dbc42bc-fbf4-4788-ba4a-985a2f457f30" + "tags": [], + "uuid": "4e856af1-f8c1-450b-a577-73e36eac3d07" }, "tool_id": null, "type": "subworkflow", @@ -3427,4 +3488,4 @@ ], "uuid": "d8fd9266-a2f8-4a6e-9c12-8d312bdd2ca7", "version": 6 -} +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md index 8efbcbfd0..5a9155f2d 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.7] 2024-07-15 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0` + ## [0.1.6] 2024-05-20 ### Automatic update From d3f92903db8dedd1572620172c9795f8dfe2d9ea Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 16 Jul 2024 17:13:48 -0400 Subject: [PATCH 2/2] Remove runtime parameters --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 81 +++---------------- 1 file changed, 10 insertions(+), 71 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index 1bdd01d79..600515db1 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -434,12 +434,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -928,20 +923,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "assembly_options" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -1101,12 +1083,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1170,12 +1147,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1286,12 +1258,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1369,12 +1336,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1648,12 +1610,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1764,12 +1721,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1892,20 +1844,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - }, - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - }, - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -3488,4 +3427,4 @@ ], "uuid": "d8fd9266-a2f8-4a6e-9c12-8d312bdd2ca7", "version": 6 -} \ No newline at end of file +}