diff --git a/CHANGELOG.md b/CHANGELOG.md index a08fac3..601124b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.12] 2024-03-25 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0` + ## [0.11] 2024-03-18 ### Automatic update diff --git a/atacseq-tests.yml b/atacseq-tests.yml index 3481b4a..d4b0b84 100644 --- a/atacseq-tests.yml +++ b/atacseq-tests.yml @@ -106,7 +106,7 @@ cutadapt: asserts: has_line: - line: "SRR891268_chr22_enriched_2\t4.6\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" + line: "SRR891268_chr22_enriched_2\t4.7\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" general_stats: asserts: has_text: diff --git a/atacseq.ga b/atacseq.ga index 5d19fe7..090533d 100644 --- a/atacseq.ga +++ b/atacseq.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.11", + "release": "0.12", "name": "ATACseq", "steps": { "0": { @@ -123,7 +123,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -173,15 +173,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0", "tool_shed_repository": { - "changeset_revision": "64172f1c1202", + "changeset_revision": "944ae523bacb", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": 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\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R2\", \"adapter\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\", \"minimum_length2\": null, \"maximum_length2\": null}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": 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": "4.6+galaxy1", + "tool_version": "4.7+galaxy0", "type": "tool", "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7", "when": null, @@ -280,12 +280,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Filter BAM", - "name": "input_bam" - } - ], + "inputs": [], "label": "filter MAPQ30 concordant pairs and not mitochondrial pairs", "name": "Filter BAM", "outputs": [ @@ -346,12 +341,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Samtools idxstats", - "name": "input" - } - ], + "inputs": [], "label": "Get number of reads per chromosome", "name": "Samtools idxstats", "outputs": [ @@ -396,12 +386,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool MarkDuplicates", - "name": "inputFile" - } - ], + "inputs": [], "label": "remove PCR duplicates", "name": "MarkDuplicates", "outputs": [ @@ -470,12 +455,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Text reformatting", - "name": "infile" - } - ], + "inputs": [], "label": "reads in chrM/MT for multiQC", "name": "Text reformatting", "outputs": [ @@ -520,12 +500,7 @@ "output_name": "outFile" } }, - "inputs": [ - { - "description": "runtime parameter for tool bedtools BAM to BED", - "name": "input" - } - ], + "inputs": [], "label": "convert BAM to BED to improve peak calling", "name": "bedtools BAM to BED", "outputs": [ @@ -577,12 +552,7 @@ "output_name": "outFile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Paired-end histogram", - "name": "input_bam" - } - ], + "inputs": [], "label": "Compute fragment length histogram", "name": "Paired-end histogram", "outputs": [ @@ -644,12 +614,7 @@ "output_name": "outFile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Samtools view", - "name": "input" - } - ], + "inputs": [], "label": "number of reads", "name": "Samtools view", "outputs": [ @@ -833,12 +798,7 @@ "output_name": "outputcnt" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": "compute 1/million reads", "name": "Compute", "outputs": [ @@ -883,12 +843,7 @@ "output_name": "output_treat_pileup" } }, - "inputs": [ - { - "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", - "name": "input1" - } - ], + "inputs": [], "label": "Bigwig from MACS2 (no norm)", "name": "Wig/BedGraph-to-bigWig", "outputs": [ @@ -943,10 +898,6 @@ { "description": "runtime parameter for tool bedtools SlopBed", "name": "genome_file_opts" - }, - { - "description": "runtime parameter for tool bedtools SlopBed", - "name": "inputA" } ], "label": "get summits +/-500kb", @@ -1000,12 +951,7 @@ "output_name": "output_tabular" } }, - "inputs": [ - { - "description": "runtime parameter for tool Search in textfiles", - "name": "infile" - } - ], + "inputs": [], "label": "summary of MACS2", "name": "Search in textfiles", "outputs": [ @@ -1065,12 +1011,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Parse parameter value", - "name": "input1" - } - ], + "inputs": [], "label": "Convert 1/million reads to parameter", "name": "Parse parameter value", "outputs": [ @@ -1109,12 +1050,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Apply rules", - "name": "input" - } - ], + "inputs": [], "label": "Isolate each bigwig do normalize not average", "name": "Apply rules", "outputs": [ @@ -1153,12 +1089,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool bedtools MergeBED", - "name": "input" - } - ], + "inputs": [], "label": "Merge summits +/-500kb", "name": "bedtools MergeBED", "outputs": [ @@ -1231,10 +1162,6 @@ { "description": "runtime parameter for tool bigwigAverage", "name": "advancedOpt" - }, - { - "description": "runtime parameter for tool bigwigAverage", - "name": "bigwigs" } ], "label": "normalize by million reads", @@ -1294,10 +1221,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool bedtools Compute both the depth and breadth of coverage", - "name": "inputA" - }, { "description": "runtime parameter for tool bedtools Compute both the depth and breadth of coverage", "name": "reduce_or_iterate" @@ -1354,12 +1277,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Text reformatting", - "name": "infile" - } - ], + "inputs": [], "label": "number of reads in peaks", "name": "Text reformatting", "outputs": [ @@ -1419,12 +1337,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": "compute 1/million reads in peaks", "name": "Compute", "outputs": [ @@ -1473,12 +1386,7 @@ "output_name": "outputcnt" } }, - "inputs": [ - { - "description": "runtime parameter for tool Concatenate datasets", - "name": "input1" - } - ], + "inputs": [], "label": "Combine number of reads in peaks with total number of reads", "name": "Concatenate datasets", "outputs": [ @@ -1517,12 +1425,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Parse parameter value", - "name": "input1" - } - ], + "inputs": [], "label": "Convert 1/million reads in peaks to parameter", "name": "Parse parameter value", "outputs": [ @@ -1561,12 +1464,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Text reformatting", - "name": "infile" - } - ], + "inputs": [], "label": "reads in peaks multiQC", "name": "Text reformatting", "outputs": [ @@ -1631,10 +1529,6 @@ { "description": "runtime parameter for tool bigwigAverage", "name": "advancedOpt" - }, - { - "description": "runtime parameter for tool bigwigAverage", - "name": "bigwigs" } ], "label": "normalize by million reads in peaks", diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 91a5dd8..7374c6e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,7 +21,7 @@ { "@id": "./", "@type": "Dataset", - "datePublished": "2024-03-19T08:15:08.617178", + "datePublished": "2024-03-25T09:46:47.919660", "hasPart": [ { "@id": "atacseq.ga" @@ -72,7 +72,7 @@ "@id": "#galaxy" }, "url": "https://github.com/iwc-workflows/atacseq", - "version": "0.11" + "version": "0.12" }, { "@id": "#galaxy",