Update for version 0.8

iwc-workflows · Oct 19, 2023 · 0c23e66 · 0c23e66
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diff --git 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
@@ -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
@@ -55,15 +55,15 @@
         SRR891268_chr22_enriched:
           asserts:
             has_n_lines: 
-              n: 255
+              n: 225
     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: 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
@@ -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
@@ -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",