diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index b801366da..d71b86cda 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog + +## [0.2.8] 2024-09-12 + +- Add suffix to the scaffold names corresponding to the haplotype being assembled + ## [0.2.7] 2024-08-13 - Expose Busco lineage database parameter diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md index 6b8eee774..e497e5704 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md @@ -16,6 +16,7 @@ Example of trajectory : 5. Concatenated HiC reverse reads [fastq] 6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0) 7. Estimated genome size [txt] +8. Haplotype name ### Outputs diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml index 233518b61..a73013131 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml @@ -19,6 +19,7 @@ Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Restriction enzymes: arima2 + Haplotype: hap1 outputs: "Reconciliated Scaffolds: gfa": asserts: @@ -28,6 +29,8 @@ asserts: has_n_lines: n: 168 + has_text: + text: "scaffold_53.hap1" Busco Summary: asserts: has_text: diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index deccec3a4..499b03b32 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -15,8 +15,8 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.7", - "name": "Scaffolding-HiC-VGP8", + "release": "0.2.8", + "name": "Scaffolding with Hi-C data VGP8", "report": { "markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary image\")\n```\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## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -38,7 +38,7 @@ "outputs": [], "position": { "left": 0, - "top": 163.55078125 + "top": 220.18215513867335 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -54,6 +54,39 @@ "errors": null, "id": 1, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Haplotype" + } + ], + "label": "Haplotype", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 10.342401705473666, + "top": 303.58456411376267 + }, + "tool_id": null, + "tool_state": "{\"restrictions\": [\"hap1\", \"hap2\", \"mat\", \"pat\", \"pri\", \"alt\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "3495a63c-bcd5-45fa-b327-ed7ec0234e78", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": 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a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md index 2e02859a8..0ae8f3667 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md +++ b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.1.2] 2024-09-19 + +### Manual update + +- Change percent identity threshold for Resfinder blast results in StarAMR from 98.0% to 90.0% + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga index 16290adad..a11f7e612 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.1", + "release": "1.1.2", "name": 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\"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced\": {\"pid_threshold\": \"90.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.10.0+galaxy1", "type": "tool", "uuid": "10eed503-9e5b-4acf-8cd8-29e81d7668a5", diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md index b7ca5db4a..53693c435 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [1.1.4] 2024-09-19 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + +## [1.1.3] 2024-09-09 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0` + ## [1.1.2] - 2024-07-19 - PlasmidFinder database correction in .ga diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga index ccb7df177..e1bbf657e 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.2", + "release": "1.1.4", "name": "bacterial_genome_annotation", "steps": { "0": { @@ -632,7 +632,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -905,15 +905,15 @@ "output_name": "summary_txt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "ba6990f72184", + "changeset_revision": "d77802fe76f7", "name": "bakta", "owner": "iuc", 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"678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6", @@ -1211,4 +1211,4 @@ ], "uuid": "d55a9e46-a205-4143-b92f-3783499063ed", "version": 1 -} +} \ No newline at end of file diff --git a/workflows/epigenetics/atacseq/CHANGELOG.md b/workflows/epigenetics/atacseq/CHANGELOG.md index 45148b198..4b0e6dc95 100644 --- a/workflows/epigenetics/atacseq/CHANGELOG.md +++ b/workflows/epigenetics/atacseq/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.17] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `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` + +### Manual update +- Add a step to remove comments lines from histogram to be compatible with new multiQC version + ## [0.16] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/atacseq/atacseq-tests.yml b/workflows/epigenetics/atacseq/atacseq-tests.yml index 133f508b1..1b2a1961d 100644 --- a/workflows/epigenetics/atacseq/atacseq-tests.yml +++ b/workflows/epigenetics/atacseq/atacseq-tests.yml @@ -98,31 +98,11 @@ value: 1133795 delta: 100000 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_line: - line: "SRR891268_chr22_enriched\t280964\t280964\t30410\t109333\t141221\t13319\t6127\t6515\t21540\t98.91\t10770.0\t3063.5\t3257.5" - cutadapt: - asserts: - has_line: - line: "SRR891268_chr22_enriched_2\t4.9\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" - general_stats: - asserts: - has_text: - text: "SRR891268_chr22_enriched\t200.0\t223\t0.028469\t98.91" - macs: - asserts: - has_line: - line: "SRR891268_chr22_enriched\t223\t47.0\t232804.0\t200.0" - picard_dups: - asserts: - has_line: - line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t119813.0\t0.0\t0.0\t0.0\t3411.0\t5.0\t0.028469\t2067029.0" - sources: - asserts: - has_n_lines: - n: 4 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_peak_count Picard: Mark Duplicates_mqc_generalstats_picard_mark_duplicates_PERCENT_DUPLICATION Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "SRR891268_chr22_enriched\t200.0\t223\t2.8[0-9]*\t98.[0-9]*\t4.7[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/workflows/epigenetics/atacseq/atacseq.ga index 6d7327a26..a885049d5 100644 --- a/workflows/epigenetics/atacseq/atacseq.ga +++ b/workflows/epigenetics/atacseq/atacseq.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will compute 2 normalization for coverage: normalized by million reads and normalized by million reads in peaks. Will plot the number of reads for each fragment length.", + "comments": [], "creator": [ { "class": "Person", @@ -10,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.16", + "release": "0.17", "name": "ATACseq", "steps": { "0": { @@ -123,7 +124,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -173,15 +174,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "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\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R2\", \"adapter\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"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\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"15": { + "16": { "annotation": "", "content_id": "wig_to_bigWig", "errors": null, - "id": 15, + "id": 16, "input_connections": { "input1": { "id": 13, @@ -879,11 +924,11 @@ } ] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0", "errors": null, - "id": 16, + "id": 17, "input_connections": { "genome_file_opts|genome": { "id": 1, @@ -940,11 +985,11 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "infile": { "id": 13, @@ -982,7 +1027,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1000,14 +1045,14 @@ } ] }, - "18": { + "19": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input1": { - "id": 14, + "id": 15, "output_name": "out_file1" } }, @@ -1039,14 +1084,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "__APPLY_RULES__", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 15, + "id": 16, "output_name": "out_file1" } }, @@ -1078,14 +1123,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "output" } }, @@ -1131,22 +1176,22 @@ } ] }, - "21": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, - "id": 21, + "id": 22, "input_connections": { "advancedOpt|binSize": { "id": 3, "output_name": "output" }, "advancedOpt|scaleFactors": { - "id": 18, + "id": 19, "output_name": "text_param" }, "bigwigs": { - "id": 19, + "id": 20, "output_name": "output" } }, @@ -1205,14 +1250,14 @@ } ] }, - "22": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0", "errors": null, - "id": 22, + "id": 23, "input_connections": { "inputA": { - "id": 20, + "id": 21, "output_name": "output" }, "reduce_or_iterate|inputB": { @@ -1266,14 +1311,14 @@ "when": null, "workflow_outputs": [] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 23, + "id": 24, "input_connections": { "infile": { - "id": 22, + "id": 23, "output_name": "output" } }, @@ -1308,7 +1353,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1326,14 +1371,14 @@ } ] }, - "24": { + "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input": { - "id": 23, + "id": 24, "output_name": "outfile" } }, @@ -1357,28 +1402,28 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": true, \"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\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "5f55e258-a4fe-4b51-ab9b-2a6f0f22d910", "when": null, "workflow_outputs": [] }, - "25": { + "26": { "annotation": "", "content_id": "cat1", "errors": null, - "id": 25, + "id": 26, "input_connections": { "input1": { - "id": 23, + "id": 24, "output_name": "outfile" }, "queries_0|input2": { @@ -1414,14 +1459,14 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input1": { - "id": 24, + "id": 25, "output_name": "out_file1" } }, @@ -1453,14 +1498,14 @@ "when": null, "workflow_outputs": [] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 27, + "id": 28, "input_connections": { "infile": { - "id": 25, + "id": 26, "output_name": "out_file1" } }, @@ -1486,7 +1531,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1498,22 +1543,22 @@ "when": null, "workflow_outputs": [] }, - "28": { + "29": { "annotation": "Isolate each bigwig do normalize not average", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "advancedOpt|binSize": { "id": 3, "output_name": "output" }, "advancedOpt|scaleFactors": { - "id": 26, + "id": 27, "output_name": "text_param" }, "bigwigs": { - "id": 19, + "id": 20, "output_name": "output" } }, @@ -1572,11 +1617,11 @@ } ] }, - "29": { + "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, - "id": 29, + "id": 30, "input_connections": { "results_0|software_cond|input": { "id": 4, @@ -1595,15 +1640,15 @@ "output_name": "metrics_file" }, "results_4|software_cond|input": { - "id": 11, - "output_name": "output2" + "id": 14, + "output_name": "output" }, "results_5|software_cond|input": { "id": 13, "output_name": "output_tabular" }, "results_6|software_cond|input": { - "id": 27, + "id": 28, "output_name": "outfile" } }, @@ -1611,10 +1656,6 @@ "label": null, "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -1622,6 +1663,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1635,15 +1680,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"chrM\", \"title\": \"reads mapping on chrM\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"linegraph\", \"section_name\": \"Fragment size\", \"title\": \"Fragment size distribution\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"Reads in peaks\", \"title\": \"Number of reads in peaks\", \"description\": \"Number of reads falling 500bp from a summit\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"chrM\", \"title\": \"reads mapping on chrM\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"linegraph\", \"section_name\": \"Fragment size\", \"title\": \"Fragment size distribution\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"Reads in peaks\", \"title\": \"Number of reads in peaks\", \"description\": \"Number of reads falling 500bp from a summit\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "112d720f-c747-4c92-985f-ebdb52086cc9", "when": null, @@ -1664,6 +1709,6 @@ "tags": [ "ATACseq" ], - "uuid": "02785f0c-c445-4419-9f95-a202eaf6493a", + "uuid": "9debc3c9-ccbd-4ce6-a7de-80580e663cac", "version": 1 } \ No newline at end of file diff --git a/workflows/epigenetics/chipseq-pe/CHANGELOG.md b/workflows/epigenetics/chipseq-pe/CHANGELOG.md index 902e9525a..b2ca81d15 100644 --- a/workflows/epigenetics/chipseq-pe/CHANGELOG.md +++ b/workflows/epigenetics/chipseq-pe/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.12] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `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` + ## [0.11] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml b/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml index 7817a8d66..30f746b1b 100644 --- a/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml +++ b/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml @@ -31,27 +31,11 @@ - that: "has_text" text: Bowtie 2 / HiSAT2 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_text: - text: "46307\t46307\t1292" - cutadapt: - asserts: - has_text: - text: "4.9\t50000\t587\t550\t3693\t46307\t5100000" - general_stats: - asserts: - has_text: - text: "201.0\t0.0\t11\t98.68" - macs: - asserts: - has_text: - text: "11\t201.0\t41724.0\t41724.0\t1.0" - sources: - asserts: - has_n_lines: - n: 3 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_treatment_redundant_rate MACS2_mqc_generalstats_macs2_peak_count Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "wt_H3K4me3\t201.0\t0.0\t11\t98.[0-9]*\t10.[0-9]*" filtered BAM: element_tests: wt_H3K4me3: diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga b/workflows/epigenetics/chipseq-pe/chipseq-pe.ga index ffeb5ecc6..d2790c119 100644 --- a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga +++ b/workflows/epigenetics/chipseq-pe/chipseq-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.11", + "release": "0.12", "name": "ChIPseq_PE", "steps": { "0": { @@ -177,7 +177,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -235,15 +235,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "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\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"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\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "c7846b4c-54fb-458e-982e-c0d8358a9f5d", "when": null, @@ -578,7 +578,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -645,7 +645,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 12, "input_connections": { @@ -666,10 +666,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -677,6 +673,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -690,15 +690,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "fb066848-43df-412a-9767-9613bac7d961", "when": null, diff --git a/workflows/epigenetics/chipseq-sr/CHANGELOG.md b/workflows/epigenetics/chipseq-sr/CHANGELOG.md index 8e0ea5d7a..8bbc5bf4e 100644 --- a/workflows/epigenetics/chipseq-sr/CHANGELOG.md +++ b/workflows/epigenetics/chipseq-sr/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.12] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `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` + ## [0.11] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml b/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml index bb6ab5373..19c00d991 100644 --- a/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml +++ b/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml @@ -22,27 +22,11 @@ - that: "has_text" text: Bowtie 2 / HiSAT2 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_text: - text: "49251\t49251\t805" - cutadapt: - asserts: - has_text: - text: "4.9\t50000\t587\t749\t49251" - general_stats: - asserts: - has_text_matching: - expression: "200.0\t0.0\t4\t98.[0-9]*\t4.612745098039215" - macs: - asserts: - has_text: - text: "4\t49.0\t44078.0\t44038.0\t1.0\t0.0\t200.0" - sources: - asserts: - has_n_lines: - n: 3 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_treatment_redundant_rate MACS2_mqc_generalstats_macs2_peak_count Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "wt_H3K4me3\t200.0\t0.0\t4\t98.[0-9]*\t4.6[0-9]*" filtered BAM: element_tests: wt_H3K4me3: diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga index 4a8cdf57b..4c3b60c6c 100644 --- a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga +++ b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.11", + "release": "0.12", "name": "ChIPseq_SR", "steps": { "0": { @@ -150,7 +150,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -204,15 +204,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"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\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "c7846b4c-54fb-458e-982e-c0d8358a9f5d", "when": null, @@ -547,7 +547,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -614,7 +614,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -635,10 +635,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -646,6 +642,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -659,15 +659,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "fb066848-43df-412a-9767-9613bac7d961", "when": null, diff --git a/workflows/epigenetics/consensus-peaks/CHANGELOG.md b/workflows/epigenetics/consensus-peaks/CHANGELOG.md index 11d873533..95a2698f7 100644 --- a/workflows/epigenetics/consensus-peaks/CHANGELOG.md +++ b/workflows/epigenetics/consensus-peaks/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.2] 2024-09-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `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` + ## [1.1] 2024-05-27 ### Automatic update diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga index aea947871..7afaa8136 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ATAC or CUTandRUN replicates", "steps": { "0": { @@ -239,7 +239,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 5, "input_connections": { @@ -268,15 +268,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "9cff58b2-123e-42df-b562-3b2a4a553934", "when": null, @@ -886,7 +886,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -989,7 +989,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 20, "input_connections": { @@ -1022,15 +1022,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "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\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "36713e3f-6110-41f7-8df1-9a9966400fab", "when": null, @@ -1226,7 +1226,7 @@ }, "24": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 24, "input_connections": { @@ -1243,13 +1243,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1263,15 +1263,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1403,7 +1403,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga index 40fa85952..6a069cc8e 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_PE replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "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\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1153,13 +1153,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1173,15 +1173,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga index 05c3c38a5..857414f3b 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_SR replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "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}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "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\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"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__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1153,13 +1153,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1173,15 +1173,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/cutandrun/CHANGELOG.md b/workflows/epigenetics/cutandrun/CHANGELOG.md index 99a77c9c8..90d5cbc5f 100644 --- a/workflows/epigenetics/cutandrun/CHANGELOG.md +++ b/workflows/epigenetics/cutandrun/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.13] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `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` + ## [0.12] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/cutandrun/cutandrun.ga b/workflows/epigenetics/cutandrun/cutandrun.ga index 570a20325..5f8a1fcb6 100644 --- a/workflows/epigenetics/cutandrun/cutandrun.ga +++ b/workflows/epigenetics/cutandrun/cutandrun.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.12", + "release": "0.13", "name": "CUTandRUN", "steps": { "0": { @@ -177,7 +177,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -235,15 +235,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "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\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - 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"tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "774b0604-628f-46a1-9088-a59d082e5317", "when": null, @@ -698,7 +698,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -765,7 +765,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -790,10 +790,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -801,6 +797,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -814,15 +814,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "0edf5e04-cc38-414c-9b57-117e919c435b", "when": null, diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md index 93fd2a18b..76ccd6b1b 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md +++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.1.2] 2024-09-19 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga index f75417bac..f9b1fd302 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga @@ -26,7 +26,7 @@ } ], "format-version": "0.1", - "release": "1.1.1", + "release": "1.1.2", "license": "GPL-3.0-or-later", "name": "Bacterial Genome Assembly using Shovill", "steps": { @@ -630,7 +630,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 19, \"input\": {\"__class__\": \"ConnectedValue\"}, \"contig_graph_path\": {\"__class__\": \"ConnectedValue\"}, \"bam_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.1.0\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"quast\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quast_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"5.2.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"refseqmasher\", \"__current_case__\": 18, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.1.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bandage\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"bandage_plot_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.8.1\", \"reference_database_version\": null}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 19, \"input\": {\"__class__\": \"ConnectedValue\"}, \"contig_graph_path\": {\"__class__\": \"ConnectedValue\"}, \"bam_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.1.0\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"quast\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quast_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"5.2.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"refseqmasher\", \"__current_case__\": 18, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.1.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bandage\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"bandage_plot_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2022.09\", \"reference_database_version\": null}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.9+galaxy0", "type": "tool", "uuid": "b6156c8e-5048-41e3-90d9-f9302734c3d1", diff --git a/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md b/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md index 41a1d7812..3299a4ba0 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md +++ b/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [1.1.2] 2024-08-05 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0` + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga index 8d3ac74fb..b83bca455 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga +++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.1", + "release": "1.1.2", "name": "Quality and Contamination Control For Genome Assembly", "steps": { "0": { @@ -131,7 +131,7 @@ "top": 454.91066885428484 }, "tool_id": null, - "tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\"], \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\", \"2020-12-03\", \"2022-03-08\", \"2024-06-05\"], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "daac0634-bcf4-4fdd-bcd2-67247f5afdd0", @@ -396,7 +396,7 @@ }, "6": { "annotation": "bracken_abundance_estimation", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -456,15 +456,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "1d4bd12f01cf", + "changeset_revision": "0c7b6eb7e752", "name": "bracken", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": {\"__class__\": \"ConnectedValue\"}, \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.9+galaxy0", + "tool_version": "3.0+galaxy0", "type": "tool", "uuid": "e088cdc6-d79b-453c-8787-6d4b7004312a", "when": null, @@ -483,7 +483,7 @@ }, "7": { "annotation": "recentrifuge_taxonomy_visualization", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -584,15 +584,15 @@ "output_name": "stat_tsv" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "76bf12b928f4", + "changeset_revision": "d4fbfd31696c", "name": "recentrifuge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": {\"__class__\": \"ConnectedValue\"}}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.14.0+galaxy0", + "tool_version": "1.14.1+galaxy0", "type": "tool", "uuid": "2db5d20e-62c7-43ad-b21f-e9992c77faa1", "when": null, @@ -718,7 +718,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.2\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.12.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.4\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.3\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.0\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.14.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.9+galaxy0", "type": "tool", "uuid": "b88b0ffe-f660-43ea-b00a-40ca0087f83f", diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md index 9771fe8a1..df831a515 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md +++ b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.5] 2024-09-25 + +### Manual update +- `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1` +- `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` + ## [0.4] 2024-04-08 ### Automatic update diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml index eb13dcea9..723587f8b 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml @@ -54,15 +54,11 @@ Number of expected cells: 500 outputs: MultiQC_STARsolo: - class: File asserts: - - that: "has_text_matching" - expression: ">subsample
3[0-9].[0-9]%
33.[0-9]%
" Seurat input for gene expression (filtered): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: @@ -79,8 +75,7 @@ has_line: line: "FBgn0250732 gfzf" CITE-seq-Count report: - class: Collection - collection_type: list + attributes: { collection_type: list } element_tests: subsample: asserts: @@ -93,8 +88,7 @@ - that: "has_line" line: "Percentage unmapped: 1" Seurat input for CMO (UMI): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga index 7ea0d5b76..04abdf111 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.", + "comments": [], "creator": [ { "class": "Person", @@ -30,7 +31,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "scRNA-seq_preprocessing_10X_cellPlex", "steps": { "0": { @@ -464,7 +465,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -572,15 +573,15 @@ "output_name": "reads_per_gene" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "42ce70172b72", + "changeset_revision": "45795f582ae9", "name": "rna_starsolo", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -588,7 +589,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -605,13 +606,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -625,15 +626,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973", "when": null, @@ -954,7 +955,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -999,7 +1000,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1044,7 +1045,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1295,8 +1296,8 @@ ] } }, - "tags": "", - "uuid": "89502a02-ec65-400c-b428-68eda7ea6b40" + "tags": [], + "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a" }, "tool_id": null, "type": "subworkflow", @@ -1311,7 +1312,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "a999ad68-faa9-4ccb-81b4-ac648af028bd" }, "tool_id": null, @@ -1534,7 +1535,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1753,7 +1754,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1798,7 +1799,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1843,7 +1844,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2094,7 +2095,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "79342c4e-bb7a-4b25-a214-7d5a10fbfd79" }, "tool_id": null, @@ -2166,6 +2167,6 @@ "tags": [ "#single-cell" ], - "uuid": "b8bd25f7-caa3-44da-8329-26dce6d46636", - "version": 4 + "uuid": "470536e7-ac58-4859-94d6-2085be9c2e17", + "version": 3 } \ No newline at end of file diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml index 82a7c4eee..dcfa61c1d 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml @@ -29,15 +29,11 @@ filetype: tabular outputs: 'MultiQC on input dataset(s): Webpage': - class: File asserts: - - that: "has_text_matching" - expression: ">subsample
3[0-9].[0-9]%
33.[0-9]%
" Seurat input for gene expression (filtered): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga index 89f7de368..dd5740b2b 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga @@ -30,7 +30,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "scRNA-seq_preprocessing_10X_v3_Bundle", "steps": { "0": { @@ -170,7 +170,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -278,15 +278,15 @@ "output_name": "reads_per_gene" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "42ce70172b72", + "changeset_revision": "45795f582ae9", "name": "rna_starsolo", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"RuntimeValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"RuntimeValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"RuntimeValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -294,7 +294,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -311,13 +311,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -331,15 +331,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973", "when": null, @@ -660,7 +660,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -705,7 +705,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -750,7 +750,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1001,8 +1001,8 @@ ] } }, - "tags": "", - "uuid": "415c1b14-3b63-4d27-8c34-42e452cb49f1" + "tags": [], + "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a" }, "tool_id": null, "type": "subworkflow", @@ -1020,6 +1020,6 @@ "tags": [ "#single-cell" ], - "uuid": "19feac09-8db7-4e3f-9774-8b815918cfa7", + "uuid": "87f25ddb-a663-4582-9ec6-d0b4bef4109c", "version": 2 } \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 80585c158..64d12ef64 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.9] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1` +- `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` + ## [0.8] 2024-07-15 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 4b3b223bc..76be417ce 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -45,23 +45,11 @@ value: 89048730 delta: 8000000 'MultiQC on input dataset(s): Stats': - element_tests: - cutadapt: - asserts: - has_text: - text: "1057657 25033 25779 25250 1032407 78266618 3650637 73538382 6.041191149974054" - general_stats: - asserts: - has_text: - text: "GSM461177 82.8 854812.0" - sources: - asserts: - has_n_lines: - n: 4 - star: - asserts: - has_text_matching: - expression: "GSM461177 1032407.0 71.0 854812.0 82.8 70.65 10276[23].0 102412.0 1020[34][0-9].0 679.0 20.0 24.0 0.54 0.0 1.56 0.0 1.43 82072.0 7.95 32881.0 3.18 0.0 5.9 0.17 0 60888 1754" + asserts: + has_line: + line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "GSM461177\t1.0[0-9]*\t0.93[0-9]*\t90.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.08[0-9]*\t6.0[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 22f14d9eb..ca98e047a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.8", + "release": "0.9", "name": "RNAseq_PE", "steps": { "0": { @@ -259,7 +259,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -315,15 +315,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "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\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"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\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "bb78142b-c185-40a6-b7c5-4fa9f6b3d314", "when": null, @@ -526,7 +526,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -616,15 +616,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "b0f2be869d6d", + "changeset_revision": "4014de1b6daf", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "8f30d1b2-6458-491b-bf46-9bdcca9db085", "when": null, @@ -648,7 +648,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -669,10 +669,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -680,6 +676,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -693,15 +693,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "da516e4c-e074-4930-a6f8-a68d9844d386", "when": null, @@ -897,7 +897,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1055,7 +1055,7 @@ } }, "tags": [], - "uuid": "c548dfba-fd18-4f89-bba4-722f9a1cc300" + "uuid": "fdfcabc8-5014-4574-85ab-0182cb11750f" }, "tool_id": null, "type": "subworkflow", @@ -1385,7 +1385,7 @@ }, "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" @@ -1434,7 +1434,7 @@ }, "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" @@ -1634,7 +1634,7 @@ } }, "tags": [], - "uuid": "3d850804-e1e9-4517-8f33-ecba0c527b73" + "uuid": "879fffe0-897e-44c2-af76-934f0a79534c" }, "tool_id": null, "type": "subworkflow", @@ -1802,7 +1802,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index d87e3c0e8..389e9e12d 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.9] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1` +- `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` + ## [0.8] 2024-07-15 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 2c0d813b7..6be85c478 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -34,24 +34,12 @@ has_size: value: 43037033 delta: 4000000 - 'MultiQC on input dataset(s): Stats': - element_tests: - cutadapt: - asserts: - has_text: - text: "\t1057657\t25033\t6191\t1051466\t39133309\t1439589\t37547108\t4.053327051898423" - general_stats: - asserts: - has_text: - text: "GSM461177\t82.86\t871202.0\t4.053327051898423" - sources: - asserts: - has_n_lines: - n: 4 - star: - asserts: - has_text_matching: - expression: "GSM461177\t1051466.0\t35.0\t871202.0\t82.86\t35.4\t51184.0\t50995.0\t50810.0\t343.0\t12.0\t19.0\t0.48\t0.0\t1.48\t0.0\t1.36\t9180[89].0\t8.73\t34515.0\t3.28\t0.0\t4.76\t0.37\t0\t5005[01]\t3890" + 'MultiQC on input dataset(s): Stats': + asserts: + has_line: + line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "GSM461177\t1.0[0-9]*\t0.96[0-9]*\t91.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.091[0-9]*\t4.0[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index b18022f50..509d68a0d 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -12,7 +12,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.8", + "release": "0.9", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", @@ -232,7 +232,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 8, "input_connections": { @@ -284,15 +284,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"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\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"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\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "4d39b70d-c852-4c42-9e0d-f3641d632543", "when": null, @@ -495,7 +495,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, "id": 13, "input_connections": { @@ -585,15 +585,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "b0f2be869d6d", + "changeset_revision": "4014de1b6daf", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "ba4d9ac2-f8b6-43bc-bc5f-e542c44441cd", "when": null, @@ -866,7 +866,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1024,7 +1024,7 @@ } }, "tags": [], - "uuid": "0af80b84-9ced-41d5-8315-40dfe8c1b638" + "uuid": "d629f889-14c9-4a3f-bf9f-1b31117e3191" }, "tool_id": null, "type": "subworkflow", @@ -1354,7 +1354,7 @@ }, "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" @@ -1403,7 +1403,7 @@ }, "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" @@ -1603,7 +1603,7 @@ } }, "tags": [], - "uuid": "7bf438af-cb14-4fd2-ba15-2e86b44ed0cb" + "uuid": "f97bb6df-6f4c-4ccd-8108-6b2d88f35ff4" }, "tool_id": null, "type": "subworkflow", @@ -1771,7 +1771,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"