diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b9b88a..4e6db01 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.8] 2023-10-19 + +Fix the remove duplicate step! +In all previous versions, due to an error, PCR duplicates were not removed. + ## [0.7] 2023-10-17 ### Automatic update diff --git a/README.md b/README.md index d43ec4e..2a58349 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ You can have more information about ATAC-seq analysis in the [slides](https://tr - The workflow will remove nextera adapters and low quality bases and filter out any read smaller than 15bp. - The filtered reads are mapped with bowtie2 allowing dovetail and fragment length up to 1kb. - The BAM is filtered to keep only MAPQ30, concordant pairs and pairs outside of the mitochondria. -- The PCR duplicates are removed with Picard. +- The PCR duplicates are removed with Picard (only from version 0.8). - 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 diff --git a/atacseq-tests.yml b/atacseq-tests.yml index b1e1aa1..49d1939 100644 --- a/atacseq-tests.yml +++ b/atacseq-tests.yml @@ -55,7 +55,7 @@ SRR891268_chr22_enriched: asserts: has_n_lines: - n: 255 + n: 225 MACS2 report: element_tests: SRR891268_chr22_enriched: @@ -63,7 +63,7 @@ - that: "has_text" text: "# tag size is determined as 47 bps" - that: "has_text" - text: "# total tags in treatment: 241306" + text: "# total tags in treatment: 234432" Coverage from MACS2 (bigwig): element_tests: SRR891268_chr22_enriched: @@ -76,13 +76,13 @@ SRR891268_chr22_enriched: asserts: has_n_lines: - n: 240 + n: 213 Nb of reads in summits +-500bp: element_tests: SRR891268_chr22_enriched: asserts: has_line: - line: "10167" + line: "8802" bigwig_norm: element_tests: SRR891268_chr22_enriched: @@ -110,11 +110,11 @@ general_stats: asserts: has_text: - text: "SRR891268_chr22_enriched\t200.0\t255\t0.028487\t98.88" + text: "SRR891268_chr22_enriched\t200.0\t225\t0.028487\t98.88" macs: asserts: has_line: - line: "SRR891268_chr22_enriched\t255\t47.0\t241306.0\t200.0" + line: "SRR891268_chr22_enriched\t225\t47.0\t234432.0\t200.0" picard_dups: asserts: has_line: diff --git a/atacseq.ga b/atacseq.ga index 4416440..c2918dc 100644 --- a/atacseq.ga +++ b/atacseq.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.7", + "release": "0.8", "name": "ATACseq", "steps": { "0": { @@ -412,7 +412,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"assume_sorted\": true, \"barcode_tag\": \"\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": false, \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"assume_sorted\": true, \"barcode_tag\": \"\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": true, \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.18.2.4", "type": "tool", "uuid": "d0a9998c-18a9-4579-8d33-f0897e1ceaeb", diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 83ac081..e90b58a 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,7 +21,7 @@ { "@id": "./", "@type": "Dataset", - "datePublished": "2023-10-17T19:52:22.592351", + "datePublished": "2023-10-19T15:11:18.072068", "hasPart": [ { "@id": "atacseq.ga" @@ -72,7 +72,7 @@ "@id": "#galaxy" }, "url": "https://github.com/iwc-workflows/atacseq", - "version": "0.7" + "version": "0.8" }, { "@id": "#galaxy", @@ -138,7 +138,7 @@ "conformsTo": { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine" }, - "engineVersion": ">=0.75.12" + "engineVersion": ">=0.75.14" }, { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",