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Workflow output definition #963

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Workflow output definition

Workflow output definition #963

GitHub Actions / JUnit Test Report failed Feb 28, 2024 in 0s

10 tests run, 0 passed, 0 skipped, 10 failed.

Annotations

Check failure on line 1 in Parameters: --nf_core_pipeline rnaseq

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline rnaseq 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/2599673342ff43612ff5d2c71e6538ee/meta/mock.nf` [condescending_joliot] DSL2 - revision: 1344f41b7b
Downloading plugin [email protected]
[27/730864] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[46/e9dcc0] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[31/cfca76] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[52/1030df] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[54/8dfa83] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[49/c52773] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[50/571749] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[b4/b4b27f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[50/f03556] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[dd/fe2cf3] Submitted process > SRA:SRA_TO_SAMPLESHEET
[1a/7bad86] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in .devcontainer

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

.Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ... 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/8b973ab156599d87f83112471195810d/meta/mock.nf` [tiny_volta] DSL2 - revision: 1344f41b7b
[a8/1782fb] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[c1/4fb9c8] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[c0/313c64] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[c4/8092bb] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[bf/45e30d] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[d5/9033ac] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[db/0b0e8d] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[15/94db9a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[8e/de7bbd] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[cc/2ee49d] Submitted process > SRA:SRA_TO_SAMPLESHEET
[c1/e69311] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --skip_fastq_download

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --skip_fastq_download 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3d6393be2180a31d0d4eaf50b073261/meta/mock.nf` [disturbed_poitras] DSL2 - revision: 1344f41b7b
[ea/3dfc02] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[9c/46cb72] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[f6/3fa76e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[33/86ce9a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[d4/9706fd] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[55/439474] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[fa/8facb6] Submitted process > SRA:SRA_TO_SAMPLESHEET
[50/68ee17] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --download_method aspera

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --download_method aspera 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/fb74b37e9342216c448289729f5f970d/meta/mock.nf` [festering_kalam] DSL2 - revision: 1344f41b7b
[47/83e5b9] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[0f/55ce90] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[c1/25983f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[18/59a345] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[60/33aeeb] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[6e/f480b6] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
[e5/d101ec] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
[dd/d74283] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[a7/85df7c] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[a5/a4a50c] Submitted process > SRA:SRA_TO_SAMPLESHEET
[19/c741b7] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline viralrecon

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline viralrecon 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/b6119d1bc44a05070663cabe6d10e8c3/meta/mock.nf` [festering_edison] DSL2 - revision: 1344f41b7b
[38/ad40f7] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[19/7f40fd] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[f6/69ab4e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[4b/54ec42] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[e5/61159b] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[c4/628fc5] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[80/396b7d] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[89/256394] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[79/923115] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[ea/3b6ff6] Submitted process > SRA:SRA_TO_SAMPLESHEET
[2b/7f4b44] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline atacseq

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline atacseq 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/7c7c71c862b2f925a2446f34a598cef7/meta/mock.nf` [suspicious_neumann] DSL2 - revision: 1344f41b7b
[91/859f98] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[fa/2e771b] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[c6/ee80b9] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[9d/5e2079] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[ae/9b51a3] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[85/63c6b3] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[a1/6c67fa] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[af/029694] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[8d/83fbf8] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[33/eecf7d] Submitted process > SRA:SRA_TO_SAMPLESHEET
[94/0363fa] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline taxprofiler

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline taxprofiler 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/373310d47d878172dd887ebfbc32cceb/meta/mock.nf` [sleepy_curry] DSL2 - revision: 1344f41b7b
[f6/a743d4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[e0/a63042] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[30/fa6e64] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[65/15e6d4] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[3e/466b2c] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[ce/7dc962] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[73/b82f6c] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[2d/1c610e] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[f8/71df89] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[fe/7efd27] Submitted process > SRA:SRA_TO_SAMPLESHEET
[6b/b9d983] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: default

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: default 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/cbeb2a3299add8cdc56b0eebd95d2296/meta/mock.nf` [drunk_boltzmann] DSL2 - revision: 1344f41b7b
[33/9cd692] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[ee/366e39] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[47/fa8187] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[e8/0d9307] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[22/980916] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[73/76b545] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[c0/0e206c] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[de/56a62b] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[01/d8c379] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[a5/2f926e] Submitted process > SRA:SRA_TO_SAMPLESHEET
[ef/32c9ed] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --download_method sratools

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --download_method sratools 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3f98fa2447097ae52f7f0c28c9fd2e5/meta/mock.nf` [trusting_monod] DSL2 - revision: 1344f41b7b
[95/297c70] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[bc/a81f89] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[9d/3b7bde] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[a2/7db6b7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[37/7c4e05] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[28/bf3660] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[e6/bb8cbd] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
[44/434729] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (DRR028935)
[ff/674801] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR9984183)
[0e/562c0d] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (ERR1160846)
[31/bf364b] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (DRX026011_DRR028935)
[87/1a3ec3] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX6725035_SRR9984183)
[20/2c4b1b] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (ERX1234253_ERR1160846)
[c4/9edc21] Submitted process > SRA:SRA_TO_SAMPLESHEET
[24/ed594d] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Should run without failures

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Should run without failures 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/74d134f23ad7be1592b6703d50788391/meta/mock.nf` [cheeky_euler] DSL2 - revision: 43c397a1ef
[a7/2cb254] Submitted process > SRA_TO_SAMPLESHEET
ERROR ~ Error executing process > 'SRA_TO_SAMPLESHEET'

Caused by:
  java.util.LinkedHashMap$Entry -- Check script '/home/runner/work/fetchngs/fetchngs/./modules/local/sra_to_samplesheet/tests/../main.nf' at line: 19

Source block:
  def records = samples.collect { meta ->
          def meta_clone = meta.clone()
          meta_clone.remove("id")
          meta_clone.remove("fastq_1")
          meta_clone.remove("fastq_2")
          meta_clone.remove("md5_1")
          meta_clone.remove("md5_2")
          meta_clone.remove("single_end")
  
          // Add relevant fields to the beginning of the map
          def record = [
              sample  : "${meta.id.split('_')[0..-2].join('_')}",
              fastq_1 : meta.fastq_1,
              fastq_2 : meta.fastq_2
          ]
  
          // Add nf-core pipeline specific entries
          if (pipeline) {
              if (pipeline == 'rnaseq') {
                  record << [ strandedness: strandedness ]
              } else if (pipeline == 'atacseq') {
                  record << [ replicate: 1 ]
              } else if (pipeline == 'taxprofiler') {
                  record << [ fasta: '' ]
              }
          }
          record << meta_clone
      }
  def samplesheet_lines = []
  samplesheet_lines << records.first().keySet().collect{ '"' + it + '"'}.join(",")
  records.each { record ->
          samplesheet_lines << record.values().collect{ '"' + it + '"'}.join(",")
      }
  def samplesheet_file = task.workDir.resolve("samplesheet.csv")
  samplesheet_file.text = samplesheet_lines.join('\n')
  def fields = mapping_fields ? ['sample'] + mapping_fields.split(',').collect{ it.trim().toLowerCase() } : []
  def mapping_lines = []
  mapping_lines << fields.collect{ '"' + it + '"'}.join(",")
  records.each { record ->
          def mappings_map = record.clone()
          if ((mappings_map.keySet() + fields).unique().size() != mappings_map.keySet().size()) {
              error("Invalid option for '--sample_mapping_fields': ${mapping_fields}.\nValid options: ${mappings_map.keySet().join(', ')}")
          }
          mapping_lines << mappings_map.subMap(fields).values().collect{ '"' + it + '"'}.join(",")
      }
  def mappings_file = task.workDir.resolve("id_mappings.csv")
  mappings_file.text = mapping_lines.join('\n')

Work dir:
  /home/runner/work/fetchngs/fetchngs/~/tests/74d134f23ad7be1592b6703d50788391/work/a7/2cb2547125bbdcf53b25af71f57976

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/fetchngs/fetchngs/~/tests/74d134f23ad7be1592b6703d50788391/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
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