Merge pull request galaxyproject#619 from lldelisle/fix_ATAC

Fix bowtie2 options in ATAC
dianichj · Nov 28, 2024 · a2e3ff9 · a2e3ff9
2 parents 6e9f186 + d980797
commit a2e3ff9
Show file tree

Hide file tree

Showing 3 changed files with 28 additions and 27 deletions.
diff --git 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
@@ -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:
@@ -55,54 +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"

diff --git 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
 }