Update for version 0.2

iwc-workflows · Nov 29, 2022 · e36373a · e36373a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,10 @@
 # Changelog
 
+## [0.2] 2022-11-28
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0`
+
 ## [0.1] 2022-10-12
 First release.
diff --git a/atacseq-tests.yml b/atacseq-tests.yml
@@ -24,11 +24,11 @@
         SRR891268_chr22_enriched:
           asserts:
             - that: "has_text"
-              text: "30410 (10.82%) aligned concordantly 0 times"
+              text: "32872 (11.70%) aligned concordantly 0 times"
             - that: "has_text"
-              text: "138163 (49.17%) aligned concordantly exactly 1 time"
+              text: "108014 (38.44%) aligned concordantly exactly 1 time"
             - that: "has_text"
-              text: "112391 (40.00%) aligned concordantly >1 times"
+              text: "140078 (49.86%) aligned concordantly >1 times"
     MarkDuplicates metrics:
       element_tests:
         SRR891268_chr22_enriched:
@@ -62,7 +62,7 @@
             - that: "has_text"
               text: "# tag size is determined as 47 bps"
             - that: "has_text"
-              text: "# total tags in treatment: 239626"
+              text: "# total tags in treatment: 241306"
     Coverage from MACS2 (bigwig):
       element_tests:
         SRR891268_chr22_enriched:
@@ -81,29 +81,29 @@
         SRR891268_chr22_enriched:
           asserts:
             has_line: 
-              line: "10107"
+              line: "10167"
     'MultiQC on input dataset(s): Stats':
       element_tests:
         bowtie2:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched\t280964\t280964\t30410\t138163\t112391\t13319\t6127\t6515\t21540\t98.91\t10770.0\t3063.5\t3257.5"
+              line: "SRR891268_chr22_enriched\t280964\t280964\t32872\t108014\t140078\t13586\t6283\t7890\t24399\t98.88\t12199.5\t3141.5\t3945.0"
         cutadapt:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched_2	4.0	285247	41011	40415	4283	280964	28524700	480633	27163516	4.771948521807416"
+              line: "SRR891268_chr22_enriched_2\t4.0\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416"
         general_stats:
           asserts:
             has_text: 
-              text: "SRR891268_chr22_enriched	200.0	255	0.028469	98.91"
+              text: "SRR891268_chr22_enriched\t200.0\t255\t0.028487\t98.88"
         macs:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched	255	47.0	239626.0	200.0"
+              line: "SRR891268_chr22_enriched\t255\t47.0\t241306.0\t200.0"
         picard_dups:
           asserts:
             has_line: 
-              line: "SRR891268_chr22_enriched	Unknown Library	0.0	119813.0	0.0	0.0	0.0	3411.0	5.0	0.028469	2067029.0"
+              line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t120653.0\t0.0\t0.0\t0.0\t3437.0\t5.0\t0.028487\t2080211.0"
         sources:
           asserts:
             has_n_lines: 

diff --git a/atacseq.ga b/atacseq.ga
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1",
+    "release": "0.2",
     "name": "ATACseq",
     "steps": {
         "0": {
@@ -93,7 +93,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -138,22 +138,22 @@
                     "output_name": "report"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "02c5a84971c8",
+                "changeset_revision": "135b80fb1ac2",
                 "name": "cutadapt",
                 "owner": "lparsons",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": \"false\"}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Nextera R2\", \"adapter2\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": \"false\"}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "4.0+galaxy0",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": \"false\"}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Nextera R2\", \"adapter2\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": \"false\"}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "4.0+galaxy1",
             "type": "tool",
             "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7",
             "workflow_outputs": []
         },
         "4": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
             "errors": null,
             "id": 4,
             "input_connections": {
@@ -204,15 +204,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "f6877ad76b00",
+                "changeset_revision": "03e9b2fbc005",
                 "name": "bowtie2",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"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_version": "2.4.5+galaxy1",
+            "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_version": "2.5.0+galaxy0",
             "type": "tool",
             "uuid": "c32a3847-f673-487f-af98-8d50999f2d21",
             "workflow_outputs": [
@@ -428,7 +428,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -484,7 +484,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"ed_score\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"split\": \"false\", \"tag\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"ed_score\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"\", \"split\": \"false\", \"tag\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.30.0+galaxy2",
             "type": "tool",
             "uuid": "12ca18f2-222b-4e9c-8ae0-b5772cd51bd7",
@@ -610,12 +610,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool MACS2 callpeak",
-                    "name": "treatment"
-                }
-            ],
+            "inputs": [],
             "label": "Call Peak with MACS2",
             "name": "MACS2 callpeak",
             "outputs": [
@@ -717,7 +712,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"advanced_options\": {\"to_large\": \"false\", \"nolambda\": \"false\", \"spmr\": \"false\", \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": \"true\"}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"all\", \"__current_case__\": 2}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BED\", \"nomodel_type\": {\"nomodel_type_selector\": \"nomodel\", \"__current_case__\": 1, \"extsize\": \"200\", \"shift\": \"-100\"}, \"outputs\": [\"peaks_tabular\", \"summits\", \"bdg\", \"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"advanced_options\": {\"to_large\": \"false\", \"nolambda\": \"false\", \"spmr\": \"false\", \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": \"true\"}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"all\", \"__current_case__\": 2}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BED\", \"nomodel_type\": {\"nomodel_type_selector\": \"nomodel\", \"__current_case__\": 1, \"extsize\": \"200\", \"shift\": \"-100\"}, \"outputs\": [\"peaks_tabular\", \"summits\", \"bdg\", \"html\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.2.7.1+galaxy0",
             "type": "tool",
             "uuid": "57386f5d-96bb-4684-97dc-3b2228189c01",
@@ -826,7 +821,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -924,7 +919,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0",
             "tool_shed_repository": {
-                "changeset_revision": "fe5b4cb8356c",
+                "changeset_revision": "a68aa6c1204a",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -985,7 +980,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0",
             "tool_shed_repository": {
-                "changeset_revision": "fe5b4cb8356c",
+                "changeset_revision": "a68aa6c1204a",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1038,7 +1033,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1130,7 +1125,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -21,7 +21,7 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "datePublished": "2022-10-20T13:35:37.242644",
+            "datePublished": "2022-11-29T12:08:35.581759",
             "hasPart": [
                 {
                     "@id": "atacseq.ga"
@@ -72,7 +72,7 @@
                 "@id": "#galaxy"
             },
             "url": "https://github.com/iwc-workflows/atacseq",
-            "version": "0.1"
+            "version": "0.2"
         },
         {
             "@id": "#galaxy",
@@ -138,7 +138,7 @@
             "conformsTo": {
                 "@id": "https://w3id.org/ro/terms/test#PlanemoEngine"
             },
-            "engineVersion": ">=0.74.11"
+            "engineVersion": ">=0.75.2"
         },
         {
             "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",