From 4be69dba3f7b3af5d76ee670d379b52277708ee6 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 13 Dec 2024 13:28:35 -0500 Subject: [PATCH 1/2] update tools --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 1231 +++++++++++------ 1 file changed, 807 insertions(+), 424 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 0c1e60942..8f944ec55 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.2", + "release": "0.2.3", "name": "Assembly-Hifi-HiC-phasing-VGP4", "report": { "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -35,15 +35,15 @@ "inputs": [ { "description": "A simple list containing PacBio data in either fasta or fastq formats.", - "name": "Pacbio Reads Collection" + "name": "Pacbio Reads" } ], - "label": "Pacbio Reads Collection", + "label": "Pacbio Reads", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 54.86661965562355 + "top": 57.703125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -54,65 +54,92 @@ "workflow_outputs": [] }, "1": { - "annotation": "Forward reads as a single dataset in fastq format", + "annotation": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\". ", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Forward reads as a single dataset in fastq format", - "name": "HiC forward reads" + "description": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\". ", + "name": "Trim Hi-C reads?" } ], - "label": "HiC forward reads", - "name": "Input dataset", + "label": "Trim Hi-C reads?", + "name": "Input parameter", "outputs": [], "position": { - "left": 5.227635768494666, - "top": 146.68167273687337 + "left": 39.140625, + "top": 149.4296875 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "d5d37559-d0fd-4d56-bb2f-a89335984a73", + "type": "parameter_input", + "uuid": "46d0bd3a-f4fd-48ab-ba51-31838a288248", "when": null, "workflow_outputs": [] }, "2": { - "annotation": "Reverse reads as a single dataset in fastq format", + "annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Reverse reads as a single dataset in fastq format", - "name": "HiC reverse reads" + "description": "", + "name": "Hi-C Forward reads" } ], - "label": "HiC reverse reads", - "name": "Input dataset", + "label": "Hi-C Forward reads", + "name": "Input dataset collection", "outputs": [], "position": { - "left": 14.512079824566827, - "top": 240.65230620636626 + "left": 62.59375, + "top": 247.1318310715006 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, - "type": "data_input", - "uuid": "94594456-f087-4983-9b0e-014e36084354", + "type": "data_collection_input", + "uuid": "294bca5c-18b5-480e-9a39-d4c484d43a21", "when": null, "workflow_outputs": [] }, "3": { - "annotation": "GenomeScope summary generated by K-mer profiling workflow", + "annotation": "", "content_id": null, "errors": null, "id": 3, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hi-C Reverse reads" + } + ], + "label": "Hi-C Reverse reads", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 75.74600104181246, + "top": 341.15748982355683 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "adbfd8c4-bfde-4545-a235-2c77f932d406", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "GenomeScope summary generated by K-mer profiling workflow", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, "inputs": [ { "description": "GenomeScope summary generated by K-mer profiling workflow", @@ -123,8 +150,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 18.350006103515625, - "top": 338.7749938964844 + "left": 90.25730560477434, + "top": 433.1059306886195 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -134,11 +161,11 @@ "when": null, "workflow_outputs": [] }, - "4": { + "5": { "annotation": "Meryl database generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 4, + "id": 5, "input_connections": {}, "inputs": [ { @@ -150,7 +177,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 37.64677777016476, + "left": 103.68703448597304, "top": 523.9735404662978 }, "tool_id": null, @@ -161,11 +188,11 @@ "when": null, "workflow_outputs": [] }, - "5": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { @@ -177,7 +204,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 81.55189123074645, + "left": 147.59214794655475, "top": 666.080035105452 }, "tool_id": null, @@ -186,19 +213,13 @@ "type": "parameter_input", "uuid": "245a5b51-c40d-4425-81ca-2baf3c157022", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "07c8cb5a-ff7f-4e51-8f81-74b2f7630f2e" - } - ] + "workflow_outputs": [] }, - "6": { + "7": { "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", "content_id": null, "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [ { @@ -210,7 +231,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 112.31427690494708, + "left": 178.35453362075538, "top": 770.3740188995779 }, "tool_id": null, @@ -219,19 +240,13 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "4c2b1889-3936-4df2-8375-250ca7dea2c7" - } - ] + "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -243,7 +258,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 122.01184397539753, + "left": 188.0521006912058, "top": 852.6092753452594 }, "tool_id": null, @@ -252,19 +267,13 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "34ed45e3-2132-4c67-af2a-b72a8cbcf55c" - } - ] + "workflow_outputs": [] }, - "8": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -276,7 +285,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 130.80851045942487, + "left": 196.84876717523315, "top": 939.8716854194543 }, "tool_id": null, @@ -285,19 +294,13 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "8c9ba587-c3e2-4200-8794-2b18ba08fc9e" - } - ] + "workflow_outputs": [] }, - "9": { + "10": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -309,7 +312,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 137.2665356894154, + "left": 203.3067924052237, "top": 1033.0113085913417 }, "tool_id": null, @@ -318,19 +321,13 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0696f3a8-cd87-4b44-a71c-54611b53be34" - } - ] + "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": null, "errors": null, - "id": 10, + "id": 11, "input_connections": {}, "inputs": [ { @@ -342,8 +339,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 145.73965411666467, - "top": 1117.6864372730274 + "left": 220.84188432960252, + "top": 1142.6599342462896 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -351,19 +348,13 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "7b3c62fb-1823-4366-92b7-053ea9054620" - } - ] + "workflow_outputs": [] }, - "11": { + "12": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", "content_id": null, "errors": null, - "id": 11, + "id": 12, "input_connections": {}, "inputs": [ { @@ -375,7 +366,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 159.833151576165, + "left": 225.87340829197328, "top": 1228.4076056463502 }, "tool_id": null, @@ -384,19 +375,13 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2e143429-f516-4a3d-8983-08df349be75f" - } - ] + "workflow_outputs": [] }, - "12": { + "13": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 12, + "id": 13, "input_connections": {}, "inputs": [ { @@ -408,7 +393,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 228.55970601638697, + "left": 294.59996273219525, "top": 1368.5129541390972 }, "tool_id": null, @@ -419,11 +404,11 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - 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"49": { + "58": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 49, + "id": 58, "input_connections": { "input": { - "id": 43, + "id": 52, "output_name": "png_files" } }, @@ -3708,7 +4091,7 @@ } ], "position": { - "left": 2607.7811628906275, + "left": 2673.821419606436, "top": 2059.98046875 }, "post_job_actions": { @@ -3732,14 +4115,14 @@ } ] }, - "50": { + "59": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 50, + "id": 59, "input_connections": { "input": { - "id": 43, + "id": 52, "output_name": "stats_files" } }, @@ -3753,7 +4136,7 @@ } ], "position": { - "left": 2894.8514753906275, + "left": 2960.891732106436, "top": 1734.2421875 }, "post_job_actions": { @@ -3777,14 +4160,14 @@ } ] }, - "51": { + "60": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 51, + "id": 60, "input_connections": { "input": { - "id": 43, + "id": 52, "output_name": "png_files" } }, @@ -3798,7 +4181,7 @@ } ], "position": { - "left": 2604.3436628906275, + "left": 2670.383919606436, "top": 2249.78125 }, "post_job_actions": { @@ -3822,14 +4205,14 @@ } ] }, - "52": { + "61": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 52, + "id": 61, "input_connections": { "infile": { - "id": 45, + "id": 54, "output_name": "output" } }, @@ -3843,7 +4226,7 @@ } ], "position": { - "left": 2973.2736415223585, + "left": 3039.313898238167, "top": 446.09145245110693 }, "post_job_actions": { @@ -3855,7 +4238,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3878,6 +4261,6 @@ "VGP", "Reviewed" ], - "uuid": "cb0e2983-13df-451c-85a2-ee78c94a2bd2", - "version": 1 + "uuid": "442c1ce7-a2b8-4d19-a19b-a3c47dcf674d", + "version": 2 } \ No newline at end of file From e8199105acd96b3dfda6e0de27b9a19246bc292a Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 13 Dec 2024 15:40:35 -0500 Subject: [PATCH 2/2] update tools --- .../Assembly-Hifi-HiC-phasing-VGP4-tests.yml | 45 +++++++++++-------- .../CHANGELOG.md | 16 +++++++ .../Assembly-Hifi-HiC-phasing-VGP4/README.md | 16 ++++--- 3 files changed, 52 insertions(+), 25 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 6c3117206..f9430e6e8 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -1,13 +1,21 @@ - doc: Test outline for Assembly-Hifi-HiC-phasing-VGP4 job: - HiC forward reads: - class: File - location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1 - filetype: fastqsanger.gz - HiC reverse reads: - class: File - location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1 - filetype: fastqsanger.gz + Hi-C Forward reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: HiC-Forward-reads + location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1 + filetype: fastqsanger.gz + Hi-C Reverse reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: HiC-Reverse-reads + location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1 + filetype: fastqsanger.gz Genomescope Model Parameters: class: File path: test-data/Genomescope Model Parameters.tabular @@ -20,7 +28,7 @@ class: File location: https://zenodo.org/records/10068595/files/Meryl%20Database.meryldb?download=1 filetype: meryldb - Pacbio Reads Collection: + Pacbio Reads: class: Collection collection_type: list elements: @@ -33,26 +41,27 @@ Name for Haplotype 2: Hap2 Homozygous Read Coverage: null Database for Busco Lineage: v5 + Trim Hi-C reads?: false outputs: - Hifiasm HiC hap1: - assert: - has_n_line: - n: 168 + Hifiasm Hi-C hap1: + asserts: + has_n_lines: + n: 114 Estimated Genome size: 2288021 Busco Summary Hap1: asserts: has_text: - text: "C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354" + text: "C:0.8%[S:0.8%,D:0.0%],F:0.3%,M:98.9%,n:3354" Nx Plot: asserts: has_size: value: 65000 delta: 10000 usable hap1 gfa: - assert: - has_n_line: - n: 173 + asserts: + has_n_lines: + n: 119 Assembly statistics for Hap1 and Hap2: asserts: has_text: - text: "# scaffolds 72 35" + text: "# scaffolds 57 51" diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 048600877..6f8dee847 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,21 @@ # Changelog +## [0.2.3] 2024-12-13 + +### Changes + +- Hi-C inputs are now entered as collections instead of single datasets +- Add optional trimming of Hi-C reads + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0` + + ## [0.2.2] 2024-08-07 - Expose parameter: Busco lineage database diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md index 1cc40e5db..1437a178a 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md @@ -5,8 +5,8 @@ Generate phased assembly based on PacBio Hifi Reads using HiC data from the same ## Inputs 1. Hifi long reads [fastq] -2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq] -3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq] +2. Collection of Hi-C forward reads [fastq] +3. Collection of Hi-C reverse reads [fastq] 4. K-mer database [meryldb] 5. Genome profile summary generated by Genomescope [txt] 6. Name of first assembly @@ -16,8 +16,10 @@ Generate phased assembly based on PacBio Hifi Reads using HiC data from the same 1. Haplotype 1 assembly ([fasta] and [gfa]) 2. Haplotype 2 assembly ([fasta] and [gfa]) -3. QC: BUSCO report for both assemblies -4. QC: Merqury report for both assemblies -5. QC: Assembly statistics for both assemblies -6. QC: Nx plot for both assemblies -7. QC: Size plot for both assemblies \ No newline at end of file +3. Trimmed Hi-C forward reads collection +4. Trimmed Hi-C reverse reads collection +5. QC: BUSCO report for both assemblies +6. QC: Merqury report for both assemblies +7. QC: Assembly statistics for both assemblies +8. QC: Nx plot for both assemblies +9. QC: Size plot for both assemblies