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Merge pull request #619 from lldelisle/fix_ATAC
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Fix bowtie2 options in ATAC
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lldelisle authored Nov 28, 2024
2 parents 6e9f186 + d980797 commit a2e3ff9
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6 changes: 6 additions & 0 deletions workflows/epigenetics/atacseq/CHANGELOG.md
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# 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
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24 changes: 12 additions & 12 deletions workflows/epigenetics/atacseq/atacseq-tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -41,7 +41,7 @@
SRR891268_chr22_enriched:
asserts:
has_size:
value: 14134105
value: 15810403
delta: 1000000
histogram of fragment length:
element_tests:
Expand All @@ -55,54 +55,54 @@
SRR891268_chr22_enriched:
asserts:
has_n_lines:
n: 223
n: 236
MACS2 report:
element_tests:
SRR891268_chr22_enriched:
asserts:
- 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"
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25 changes: 10 additions & 15 deletions workflows/epigenetics/atacseq/atacseq.ga
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.17",
"release": "1.0",
"name": "ATACseq",
"steps": {
"0": {
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
]
},
Expand Down Expand Up @@ -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": [
Expand All @@ -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",
Expand Down Expand Up @@ -1709,6 +1704,6 @@
"tags": [
"ATACseq"
],
"uuid": "9debc3c9-ccbd-4ce6-a7de-80580e663cac",
"uuid": "747f2432-7493-44b8-a5ee-82d104407cad",
"version": 1
}

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