From 3a3408ffa011839db612e73407ad9b19b2f2005b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 19 May 2023 17:00:07 +0200 Subject: [PATCH] add mapping wf test --- bin/list-workflows-with-tests.rb | 25 + .../mapping/workflows/mapping.eu.json | 1730 +++++++++++++++++ 2 files changed, 1755 insertions(+) create mode 100755 bin/list-workflows-with-tests.rb create mode 100644 topics/sequence-analysis/tutorials/mapping/workflows/mapping.eu.json diff --git a/bin/list-workflows-with-tests.rb b/bin/list-workflows-with-tests.rb new file mode 100755 index 0000000000000..9664cde682092 --- /dev/null +++ b/bin/list-workflows-with-tests.rb @@ -0,0 +1,25 @@ +#!/usr/bin/env ruby +# frozen_string_literal: true + +require 'json' +require 'yaml' + +Dir.glob('./topics/**/*.ga') do |path| + folder = File.dirname(path) + basename = File.basename(path).gsub(/.ga$/, '') + possible_tests = Dir.glob("#{folder}/#{basename}*ym*") + possible_tests = possible_tests.grep(/#{basename}[_-]tests?.ya?ml/) + + possible_tests.each do |possib| + if ! possib.match(/-test.yml/) + puts "Renaming #{possib}" + # Rename the file to have the correct extension + File.rename(possib, possib.gsub(/[_-]tests?.ya?ml$/, '-test.yml')) + end + end + + if ! possible_tests.empty? + puts "#{path}" + end + +end diff --git a/topics/sequence-analysis/tutorials/mapping/workflows/mapping.eu.json b/topics/sequence-analysis/tutorials/mapping/workflows/mapping.eu.json new file mode 100644 index 0000000000000..2ed093d41367c --- /dev/null +++ b/topics/sequence-analysis/tutorials/mapping/workflows/mapping.eu.json @@ -0,0 +1,1730 @@ +{ + "summary": { + "num_errors": 0, + "num_failures": 0, + "num_skips": 0, + "num_tests": 1 + }, + "tests": [ + { + "data": { + "end_datetime": "2023-05-19T16:33:47.079379", + "inputs": "---\nreads_1:\n class: File\n location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz\nreads_2:\n class: File\n location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read2.fastq.gz\n", + "invocation_details": { + "details": { + "error_message": "", + "history_id": "2e96b0bf6abd6b74", + "history_state": "ok", + "invocation_id": "6284e34d09b1b06d", + "invocation_state": "scheduled", + "workflow_id": "507e9a109418ad9c" + }, + "steps": { + "0. reads_1": { + "action": null, + "id": "239cd24984e05a43", + "job_id": null, + "jobs": [], + "model_class": "WorkflowInvocationStep", + "order_index": 0, + "output_collections": {}, + "outputs": { + "output": { + "id": "4838ba20a6d86765ce9b5492a01ba912", + "src": "hda", + "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8" + } + }, + "state": "scheduled", + "subworkflow": null, + "subworkflow_invocation_id": null, + "update_time": "2023-05-19T14:30:12.217904", + "workflow_step_id": "a07c7d9026192889", + "workflow_step_label": "reads_1", + "workflow_step_uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220" + }, + "1. reads_2": { + "action": null, + "id": "1da8d9ea66ac45a3", + "job_id": null, + "jobs": [], + "model_class": "WorkflowInvocationStep", + "order_index": 1, + "output_collections": {}, + "outputs": { + "output": { + "id": "4838ba20a6d8676511241aa0be025fbe", + "src": "hda", + "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c" + } + }, + "state": "scheduled", + "subworkflow": null, + "subworkflow_invocation_id": null, + "update_time": "2023-05-19T14:30:12.217908", + "workflow_step_id": "8b783f04ae56b16d", + "workflow_step_label": "reads_2", + "workflow_step_uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6" + }, + "2. 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"__input_ext": "\"input\"", + "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"", + "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", + "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", + "singlePaired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 137415404, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 137415461, \"src\": \"hda\"}]}, \"sPaired\": \"paired\", \"three_prime_clip_R1\": null, \"three_prime_clip_R2\": null, \"trim1\": false, \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}" + }, + "state": "ok", + "stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 14,011 (28.0%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 34,012 bp (1.3%)\nTotal written (filtered): 2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.3%\n C: 33.3%\n G: 24.8%\n T: 14.6%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 13,787 (27.6%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 120,340 bp (4.7%)\nTotal written (filtered): 2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.6%\n C: 32.8%\n G: 24.6%\n T: 15.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n", + "stdout": "1.13\n", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", + "tool_stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 14,011 (28.0%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 34,012 bp (1.3%)\nTotal written (filtered): 2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.3%\n C: 33.3%\n G: 24.8%\n T: 14.6%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 13,787 (27.6%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 120,340 bp (4.7%)\nTotal written (filtered): 2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.6%\n C: 32.8%\n G: 24.6%\n T: 15.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n", + "tool_stdout": "1.13\n", + "traceback": null, + "update_time": "2023-05-19T14:31:12.868610", + "user_email": "hxr@informatik.uni-freiburg.de" + } + ], + "model_class": "WorkflowInvocationStep", + "order_index": 4, + "output_collections": {}, + "outputs": { + "trimmed_reads_pair1": { + "id": "4838ba20a6d86765439b06bcf8677007", + "src": "hda", + "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf" + }, + "trimmed_reads_pair2": { + "id": "4838ba20a6d867658f72f66dd1d7e6cc", + "src": "hda", + "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e" + } + }, + "state": "scheduled", + "subworkflow": null, + "subworkflow_invocation_id": null, + "update_time": "2023-05-19T14:31:12.847743", + "workflow_step_id": "0cdaaf28f2c92138", + "workflow_step_label": null, + "workflow_step_uuid": "ba2566a8-447f-45ed-98d1-1fd1a5ba6ab4" + }, + "5. 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