diff --git a/workflows/epigenetics/atacseq/CHANGELOG.md b/workflows/epigenetics/atacseq/CHANGELOG.md index 4b0e6dc95..9d54c6b4e 100644 --- a/workflows/epigenetics/atacseq/CHANGELOG.md +++ b/workflows/epigenetics/atacseq/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.0] 2024-11-28 + +### Manual update + +Use the options like written in the README: in all previous versions, bowtie2 was running with `--very-sensitive` option but without allowing dovetail and without fragment length up to 1kb. Bowtie2 has been adjusted and is now running with these options: allow dovetail and fragment length up to 1kb. + ## [0.17] 2024-09-23 ### Automatic update diff --git a/workflows/epigenetics/atacseq/atacseq-tests.yml b/workflows/epigenetics/atacseq/atacseq-tests.yml index 1b2a1961d..7b8c713a4 100644 --- a/workflows/epigenetics/atacseq/atacseq-tests.yml +++ b/workflows/epigenetics/atacseq/atacseq-tests.yml @@ -25,11 +25,11 @@ SRR891268_chr22_enriched: asserts: - that: "has_text" - text: "30410 (10.82%) aligned concordantly 0 times" + text: "7282 (2.59%) aligned concordantly 0 times" - that: "has_text" - text: "109333 (38.91%) aligned concordantly exactly 1 time" + text: "121059 (43.09%) aligned concordantly exactly 1 time" - that: "has_text" - text: "141221 (50.26%) aligned concordantly >1 times" + text: "152623 (54.32%) aligned concordantly >1 times" MarkDuplicates metrics: element_tests: SRR891268_chr22_enriched: @@ -41,7 +41,7 @@ SRR891268_chr22_enriched: asserts: has_size: - value: 14134105 + value: 15810403 delta: 1000000 histogram of fragment length: element_tests: @@ -55,7 +55,7 @@ SRR891268_chr22_enriched: asserts: has_n_lines: - n: 223 + n: 236 MACS2 report: element_tests: SRR891268_chr22_enriched: @@ -63,46 +63,46 @@ - that: "has_text" text: "# tag size is determined as 47 bps" - that: "has_text" - text: "# total tags in treatment: 232804" + text: "# total tags in treatment: 262080" Coverage from MACS2 (bigwig): element_tests: SRR891268_chr22_enriched: asserts: has_size: - value: 2594908 + value: 2892925 delta: 200000 1kb around summits: element_tests: SRR891268_chr22_enriched: asserts: has_n_lines: - n: 211 + n: 217 Nb of reads in summits +-500bp: element_tests: SRR891268_chr22_enriched: asserts: has_line: - line: "8698" + line: "9548" bigwig_norm: element_tests: SRR891268_chr22_enriched: asserts: has_size: - value: 1130014 + value: 1253177 delta: 100000 bigwig_norm2: element_tests: SRR891268_chr22_enriched: asserts: has_size: - value: 1133795 + value: 1248419 delta: 100000 'MultiQC on input dataset(s): Stats': 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]*" + expression: "SRR891268_chr22_enriched\t200.0\t236\t2.7[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 a885049d5..664948390 100644 --- a/workflows/epigenetics/atacseq/atacseq.ga +++ b/workflows/epigenetics/atacseq/atacseq.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.17", + "release": "1.0", "name": "ATACseq", "steps": { "0": { @@ -257,7 +257,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"yes\", \"__current_case__\": 0, \"I\": \"0\", \"X\": \"1000\", \"fr_rf_ff\": \"--fr\", \"no_mixed\": false, \"no_discordant\": false, \"dovetail\": true, \"no_contain\": false, \"no_overlap\": false}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.5.3+galaxy1", "type": "tool", "uuid": "c32a3847-f673-487f-af98-8d50999f2d21", @@ -433,15 +433,15 @@ "uuid": "d0a9998c-18a9-4579-8d33-f0897e1ceaeb", "when": null, "workflow_outputs": [ - { - "label": "BAM filtered rmDup", - "output_name": "outFile", - "uuid": "5f4d5cc5-c2f2-40f3-b941-df5dd7347d25" - }, { "label": "MarkDuplicates metrics", "output_name": "metrics_file", "uuid": "144745aa-8898-45e6-a328-53e2518202b9" + }, + { + "label": "BAM filtered rmDup", + "output_name": "outFile", + "uuid": "5f4d5cc5-c2f2-40f3-b941-df5dd7347d25" } ] }, @@ -799,12 +799,7 @@ "output_name": "output2" } }, - "inputs": [ - { - "description": "runtime parameter for tool Search in textfiles", - "name": "infile" - } - ], + "inputs": [], "label": "remove comments lines", "name": "Search in textfiles", "outputs": [ @@ -825,7 +820,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"invert\": \"-v\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "c06960f8-9d4e-483e-8f07-12976f8b802a", @@ -1709,6 +1704,6 @@ "tags": [ "ATACseq" ], - "uuid": "9debc3c9-ccbd-4ce6-a7de-80580e663cac", + "uuid": "747f2432-7493-44b8-a5ee-82d104407cad", "version": 1 } \ No newline at end of file