diff --git a/.dockstore.yml b/.dockstore.yml index 72bd2a4..f0bbe43 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -1,7 +1,11 @@ version: 1.2 workflows: - name: main - primaryDescriptorPath: /atacseq.ga subclass: Galaxy + publish: true + primaryDescriptorPath: /atacseq.ga testParameterFiles: - /atacseq-tests.yml + authors: + - name: Lucille Delisle + orcid: 0000-0002-1964-4960 diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a63ffe..c6d4823 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.5] 2023-03-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4` +- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` + +### Manual update +- add normalization steps for coverage + ## [0.4] 2023-01-16 ### Automatic update diff --git a/README.md b/README.md index fe6c6bb..d43ec4e 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,7 @@ You can have more information about ATAC-seq analysis in the [slides](https://tr - reference_genome: this field will be adapted to the genomes available for bowtie2 and the genomes available for bedtools slopbed (dbkeys table) - effective_genome_size: this is used by macs2 and may be entered manually (indications are provided for heavily used genomes) +- bin_size: this is used when normalization of coverage is performed. Large values will allow to have smaller output files but with less resolution while small values will increase computation time and size of output files to produce more resolutive bigwigs. ## Processing @@ -21,7 +22,10 @@ You can have more information about ATAC-seq analysis in the [slides](https://tr - The BAM is converted to BED to enable macs2 to take both pairs into account. - The peaks are called with macs2 which at the same time generates a coverage file. - The coverage file is converted to bigwig -- The amount of reads 500bp from summits and the total number of reads are computed if further normalization is wanted. +- The amount of reads 500bp from summits and the total number of reads are computed. +- Two normalizations are computed: + - By million reads + - By million reads in peaks (500bp from summits) - Other QC are performed: - A histogram with fragment length is computed. - The evaluation of percentage of reads to chrM or MT is computed. @@ -29,5 +33,4 @@ You can have more information about ATAC-seq analysis in the [slides](https://tr ### Warning -- The coverage output is not normalized. - The `reference_genome` parameter value is used to select references in bowtie2 and bedtools slopbed. Only references that are present in bowtie2 **and** bedtools slopbed are selectable. If your favorite reference genome is not available ask your administrator to make sure that each bowtie2 reference has a corresponding len file for use in bedtools slopbed. diff --git a/atacseq-tests.yml b/atacseq-tests.yml index 628d01d..b1e1aa1 100644 --- a/atacseq-tests.yml +++ b/atacseq-tests.yml @@ -17,7 +17,8 @@ location: https://zenodo.org/record/3862793/files/SRR891268_chr22_enriched_R2.fastq.gz filetype: fastqsanger reference_genome: hg19 - effective_genome_size: '2700000000' + effective_genome_size: 2700000000 + bin_size: 1000 outputs: mapping stats: element_tests: @@ -82,6 +83,20 @@ asserts: has_line: line: "10167" + bigwig_norm: + element_tests: + SRR891268_chr22_enriched: + asserts: + has_size: + value: 1130014 + delta: 100000 + bigwig_norm2: + element_tests: + SRR891268_chr22_enriched: + asserts: + has_size: + value: 1133795 + delta: 100000 'MultiQC on input dataset(s): Stats': element_tests: bowtie2: @@ -91,7 +106,7 @@ cutadapt: asserts: has_line: - line: "SRR891268_chr22_enriched_2\t4.0\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" + line: "SRR891268_chr22_enriched_2\t4.4\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" general_stats: asserts: has_text: diff --git a/atacseq.ga b/atacseq.ga index ddf9f12..0e73185 100644 --- a/atacseq.ga +++ b/atacseq.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow take 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 plot the number of reads for each fragment length.", + "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.", "creator": [ { "class": "Person", @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "ATACseq", "steps": { "0": { @@ -37,6 +37,7 @@ "tool_version": null, "type": "data_collection_input", "uuid": "3b1d869d-e8a9-49d9-894c-8aa500cd445d", + "when": null, "workflow_outputs": [] }, "1": { @@ -63,6 +64,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "c085055c-9d18-49d7-9f87-fae61683d775", + "when": null, "workflow_outputs": [] }, "2": { @@ -89,13 +91,41 @@ "tool_version": null, "type": "parameter_input", "uuid": "43f5c231-ed56-4cda-bd50-0495dfd77d70", + "when": null, "workflow_outputs": [] }, "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "annotation": "Bin size for normalized bigwig (usually 50bp is sufficient)", + "content_id": null, "errors": null, "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "Bin size for normalized bigwig (usually 50bp is sufficient)", + "name": "bin_size" + } + ], + "label": "bin_size", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 155.54247082439377, + "top": 898.8496207394044 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "942c77e6-f462-49ac-87ed-6e4e14589b0b", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", + "errors": null, + "id": 4, "input_connections": { "library|input_1": { "id": 0, @@ -138,27 +168,28 @@ "output_name": "report" } }, - 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{ - "label": "MultiQC on input dataset(s): Stats", - "output_name": "stats", - "uuid": "6071150d-48db-4cf8-bfed-2cbdb2635856" - }, { "label": "MultiQC webpage", "output_name": "html_report", "uuid": "c22aafb2-d9f2-43c3-a6c4-cfe4a3166c07" + }, + { + "label": "MultiQC on input dataset(s): Stats", + "output_name": "stats", + "uuid": "6071150d-48db-4cf8-bfed-2cbdb2635856" } ] } @@ -1227,6 +1576,6 @@ "tags": [ "ATACseq" ], - "uuid": "eb8e9537-3716-43ea-8e07-afb56a7865cb", - "version": 25 + "uuid": "267a6009-2a4a-4c69-869c-739894a55a70", + "version": 4 } \ No newline at end of file diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d95755f..4046af2 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,7 +21,7 @@ { "@id": "./", "@type": "Dataset", - "datePublished": "2023-01-16T17:00:18.505110", + "datePublished": "2023-08-31T11:09:22.704427", "hasPart": [ { "@id": "atacseq.ga" @@ -40,7 +40,7 @@ }, "mentions": [ { - "@id": "#test1" + "@id": "#test_main_1" } ], "name": "atacseq/main" @@ -72,7 +72,7 @@ "@id": "#galaxy" }, "url": "https://github.com/iwc-workflows/atacseq", - "version": "0.4" + "version": "0.5" }, { "@id": "#galaxy", @@ -96,25 +96,25 @@ "@type": "File" }, { - "@id": "#test1", + "@id": "#test_main_1", "@type": "TestSuite", "definition": { "@id": "atacseq-tests.yml" }, "instance": [ { - "@id": "#test1_1" + "@id": "#test_main_1_1" } ], "mainEntity": { "@id": "atacseq.ga" }, - "name": "test1" + "name": "test_main_1" }, { - "@id": "#test1_1", + "@id": "#test_main_1_1", "@type": "TestInstance", - "name": "test1_1", + "name": "test_main_1_1", "resource": "repos/iwc-workflows/atacseq/actions/workflows/wftest.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" @@ -138,7 +138,7 @@ "conformsTo": { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine" }, - "engineVersion": ">=0.75.3" + "engineVersion": ">=0.75.9" }, { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",