From 73da7907be646016a94728be01906f22418174ce Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 23 Apr 2024 12:35:45 -0400 Subject: [PATCH] update cutadapt --- .../Assembly-Hifi-only-VGP3.ga | 101 ++++++------------ .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 8 ++ 2 files changed, 38 insertions(+), 71 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index c37f49842..7a785e05d 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.4", + "release": "0.1.5", "name": "Assembly-Hifi-only-VGP3", "steps": { "0": { @@ -34,7 +34,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 549.7803459425681 }, "tool_id": null, @@ -124,13 +124,7 @@ "type": "parameter_input", "uuid": "3ce6ecc2-3262-4695-b4ef-1a58f52a48bd", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "eb6539b5-84f1-4a55-906a-e1dada745409" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -157,13 +151,7 @@ "type": "parameter_input", "uuid": "1e16198c-a515-4b6d-9a72-d1de93974d2b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "48ba5562-b3eb-4e8f-82f3-83f6436da6a9" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -217,13 +205,7 @@ "type": "parameter_input", "uuid": "df030d72-fca9-4b7e-b58b-dcd27c453543", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9a6c9fbe-757b-4a7e-8b69-896e4a35b6d6" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -250,13 +232,7 @@ "type": "data_input", "uuid": "b7958e14-2495-4d38-8da1-ea583f5ae8e2", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "70dc3f0f-18af-4dad-9e5b-96d9669af408" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "", @@ -283,13 +259,7 @@ "type": "parameter_input", "uuid": "163c033f-85ce-46e5-b00a-3b3904dea278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "95517f19-9c34-4374-8439-3273b414dd88" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -316,17 +286,11 @@ "type": "parameter_input", "uuid": "88e40054-8605-4746-b91b-38ff85c70fd6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e15697b0-756e-4b6f-a52a-a8eece196e37" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0", "errors": null, "id": 10, "input_connections": { @@ -357,6 +321,11 @@ "top": 992.890625 }, "post_job_actions": { + "HideDatasetActionjson_stats": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "json_stats" + }, "TagDatasetActionout1": { "action_arguments": { "tags": "trimmed_" @@ -365,15 +334,15 @@ "output_name": "out1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "944ae523bacb", + "changeset_revision": "b1c926deaa2d", "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\": null, \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_cassava\": false}, \"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}]}}, \"output_selector\": [\"report\", \"json_stats\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": 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": "4.7+galaxy0", + "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\": null, \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"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}]}}, \"output_selector\": [\"report\", \"json_stats\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": 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": "4.8+galaxy0", "type": "tool", "uuid": "f679b5eb-cc26-4005-9499-3ad2eb4698d4", "when": null, @@ -501,7 +470,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "0203b86a-9457-48fc-87af-e251b24bad2b", @@ -639,7 +608,7 @@ } }, "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"columnList\": \"c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.2", "type": "tool", "uuid": "fb6d8a81-7921-4b8b-be3c-e6f37772caa9", @@ -719,7 +688,7 @@ } }, "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"RuntimeValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", "type": "tool", "uuid": "65b07e97-c8ea-4fbb-b37e-aab4c93c61fa", @@ -966,7 +935,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"set\", \"__current_case__\": 1, \"hifiasm_kmer_length\": \"51\", \"window_size\": \"51\", \"drop_kmers\": \"5.0\", \"max_overlaps\": \"100\", \"correction_rounds\": \"3\", \"min_hist_cnt\": null, \"max_kocc\": \"20000\", \"hg_size\": \"\"}, \"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\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"RuntimeValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"set\", \"__current_case__\": 1, \"hifiasm_kmer_length\": \"51\", \"window_size\": \"51\", \"drop_kmers\": \"5.0\", \"max_overlaps\": \"100\", \"correction_rounds\": \"3\", \"min_hist_cnt\": null, \"max_kocc\": \"20000\", \"hg_size\": \"\"}, \"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\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.19.8+galaxy1", "type": "tool", "uuid": "cecbcd76-97f0-4e7a-9c90-061d3e5be432", @@ -1560,7 +1529,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", @@ -1690,11 +1659,6 @@ "uuid": "da32529d-f84c-4af6-b443-eddfc1705d78", "when": null, "workflow_outputs": [ - { - "label": "Merqury completeness stats", - "output_name": "stats_files", - "uuid": "640107ca-7175-4624-9851-33911c197b18" - }, { "label": "Merqury png", "output_name": "png_files", @@ -1704,6 +1668,11 @@ "label": "Merqury Histograms", "output_name": "hist_files", "uuid": "9bb427f1-2afd-4e63-b7a1-2c9b54c6bee0" + }, + { + "label": "Merqury completeness stats", + "output_name": "stats_files", + "uuid": "640107ca-7175-4624-9851-33911c197b18" } ] }, @@ -3149,21 +3118,11 @@ "uuid": "08a613ce-a4c1-46df-930c-153b491114d2", "when": null, "workflow_outputs": [ - { - "label": null, - "output_name": "3:output", - "uuid": "4dcd2aff-fbe3-4471-9913-1495e27a19cf" - }, { "label": "Nx Plot", "output_name": "Nx Plot", "uuid": "e34782d2-17d1-4598-92d1-93ca3d7ec7dc" }, - { - "label": null, - "output_name": "2:output", - "uuid": "9366eaf9-0b1d-4a64-8cb8-75e10f47d8b3" - }, { "label": "Size Plot", "output_name": "Size Plot", @@ -3176,6 +3135,6 @@ "VGP", "Reviewed" ], - "uuid": "7a7986c0-d9d5-42cf-b7a8-4049c943d68c", - "version": 0 + "uuid": "f6f4cac5-6900-440b-8f1d-52420f635420", + "version": 1 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md index 3c2deb861..5d4bfe381 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog + +## [0.1.5] 2024-04-23 + +### Manual update + +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0` + + ## [0.1.4] 2024-04-19 ### Manual Updates