Update for version 0.10

iwc-workflows · Mar 14, 2024 · 3486b90 · 3486b90
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diff --git a/.github/workflows/wftest.yml b/.github/workflows/wftest.yml
@@ -10,7 +10,7 @@ jobs:
     with:
       python-version-list: "[\"3.7\"]"
       galaxy-fork: galaxyproject
-      galaxy-branch: release_23.1
+      galaxy-branch: release_23.2
   test:
     name: Test workflow
     needs: setup
@@ -19,6 +19,6 @@ jobs:
       galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
       python-version-list: "[\"3.7\"]"
       galaxy-fork: galaxyproject
-      galaxy-branch: release_23.1
+      galaxy-branch: release_23.2
       repository-list: '.'
       check-outputs: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,16 @@
 # Changelog
 
+## [0.10] 2024-03-14
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5`
+- `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0`
+
 ## [0.9] 2023-10-23
 
 Fix the normalization factor. It was coverage per reads and per reads in peaks instead of per million reads and per million reads in peaks.

diff --git a/atacseq-tests.yml b/atacseq-tests.yml
@@ -25,11 +25,11 @@
         SRR891268_chr22_enriched:
           asserts:
             - that: "has_text"
-              text: "32872 (11.70%) aligned concordantly 0 times"
+              text: "30410 (10.82%) aligned concordantly 0 times"
             - that: "has_text"
-              text: "108014 (38.44%) aligned concordantly exactly 1 time"
+              text: "109333 (38.91%) aligned concordantly exactly 1 time"
             - that: "has_text"
-              text: "140078 (49.86%) aligned concordantly >1 times"
+              text: "141221 (50.26%) aligned concordantly >1 times"
     MarkDuplicates metrics:
       element_tests:
         SRR891268_chr22_enriched:
@@ -55,15 +55,15 @@
         SRR891268_chr22_enriched:
           asserts:
             has_n_lines: 
-              n: 225
+              n: 223
     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: 234432"
+              text: "# total tags in treatment: 232804"
     Coverage from MACS2 (bigwig):
       element_tests:
         SRR891268_chr22_enriched:
@@ -76,13 +76,13 @@
         SRR891268_chr22_enriched:
           asserts:
             has_n_lines: 
-              n: 213
+              n: 211
     Nb of reads in summits +-500bp:
       element_tests:
         SRR891268_chr22_enriched:
           asserts:
             has_line: 
-              line: "8802"
+              line: "8698"
     bigwig_norm:
       element_tests:
         SRR891268_chr22_enriched:
@@ -102,23 +102,23 @@
         bowtie2:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched\t280964\t280964\t32872\t108014\t140078\t13586\t6283\t7890\t24399\t98.88\t12199.5\t3141.5\t3945.0"
+              line: "SRR891268_chr22_enriched\t280964\t280964\t30410\t109333\t141221\t13319\t6127\t6515\t21540\t98.91\t10770.0\t3063.5\t3257.5"
         cutadapt:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched_2\t4.4\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416"
+              line: "SRR891268_chr22_enriched_2\t4.6\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416"
         general_stats:
           asserts:
             has_text: 
-              text: "SRR891268_chr22_enriched\t200.0\t225\t0.028487\t98.88"
+              text: "SRR891268_chr22_enriched\t200.0\t223\t0.028469\t98.91"
         macs:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched\t225\t47.0\t234432.0\t200.0"
+              line: "SRR891268_chr22_enriched\t223\t47.0\t232804.0\t200.0"
         picard_dups:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t120653.0\t0.0\t0.0\t0.0\t3437.0\t5.0\t0.028487\t2080211.0"
+              line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t119813.0\t0.0\t0.0\t0.0\t3411.0\t5.0\t0.028469\t2067029.0"
         sources:
           asserts:
             has_n_lines: