Skip to content
nf-core CI

Workflow output definition #963

Sign in to view logs

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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/2599673342ff43612ff5d2c71e6538ee/meta/mock.nf` [intergalactic_ekeblad] DSL2 - revision: 1344f41b7b
Downloading plugin [email protected]
[3f/53d94c] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[7d/176d48] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[1f/b1cc9f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[d7/d80ee4] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[4d/150778] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[ca/2c74f5] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[67/61f3ef] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[b2/eba1a4] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[93/ebc662] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[e2/6517ec] Submitted process > SRA:SRA_TO_SAMPLESHEET
[29/97b1f1] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/8b973ab156599d87f83112471195810d/meta/mock.nf` [serene_kalman] DSL2 - revision: 1344f41b7b
[99/5472b8] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[72/fb741f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[9a/294ea1] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[43/cc15d8] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[53/81081c] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[7c/9f894c] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[ad/7dbe24] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[ca/e196a2] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[26/1f9d1b] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[bf/506e30] Submitted process > SRA:SRA_TO_SAMPLESHEET
[5d/9e494b] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3d6393be2180a31d0d4eaf50b073261/meta/mock.nf` [shrivelled_church] DSL2 - revision: 1344f41b7b
[1f/ffcde4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[a2/4f6b00] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[be/8c4fe4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[ec/de04bb] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[2e/6b3fe6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[3b/1dd7b7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[18/e3290a] Submitted process > SRA:SRA_TO_SAMPLESHEET
[a0/9a2ee2] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/fb74b37e9342216c448289729f5f970d/meta/mock.nf` [cranky_bell] DSL2 - revision: 1344f41b7b
[16/275aa2] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[83/1896e6] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[f0/d18928] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[df/9e6aa6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[12/e5dd68] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[6c/a3327d] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[17/a6dfa2] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
[62/e3b5b6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[cd/123e51] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
[10/1ecf9d] Submitted process > SRA:SRA_TO_SAMPLESHEET
[16/7349c0] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/b6119d1bc44a05070663cabe6d10e8c3/meta/mock.nf` [peaceful_lagrange] DSL2 - revision: 1344f41b7b
[d1/28846c] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[d1/0935d4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[41/948513] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[b2/8783bc] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[55/8b592f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[ba/396acb] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[67/bd7cac] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[7e/3d42f9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[3f/634f18] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[42/f9b5a1] Submitted process > SRA:SRA_TO_SAMPLESHEET
[d0/fa29f1] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/7c7c71c862b2f925a2446f34a598cef7/meta/mock.nf` [berserk_hamilton] DSL2 - revision: 1344f41b7b
[73/d3d770] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[ed/bbaa0f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[92/b372ac] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[41/52efcf] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[63/ce5586] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[03/ee61b2] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[3f/119da3] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[ad/6b0398] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[3b/8c913b] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[47/0afa28] Submitted process > SRA:SRA_TO_SAMPLESHEET
[a4/e13b6e] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/373310d47d878172dd887ebfbc32cceb/meta/mock.nf` [nice_almeida] DSL2 - revision: 1344f41b7b
[f1/fdc575] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[95/a519e3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[82/3e879f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[6f/34e2a5] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[56/77cdc8] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[10/2db8ae] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[73/9339e7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[98/b7faf1] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[aa/14babc] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[f1/a5b8e0] Submitted process > SRA:SRA_TO_SAMPLESHEET
[c9/4676d1] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/cbeb2a3299add8cdc56b0eebd95d2296/meta/mock.nf` [serene_meninsky] DSL2 - revision: 1344f41b7b
[6c/9dc2cc] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[ff/849539] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[bc/c63619] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[8a/0644ec] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[9b/6ccecb] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[d6/0c2bb1] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[a5/d9dfa0] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[98/710733] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[a0/31ac0f] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[d0/ff5958] Submitted process > SRA:SRA_TO_SAMPLESHEET
[e3/9a4a2b] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3f98fa2447097ae52f7f0c28c9fd2e5/meta/mock.nf` [mighty_volhard] DSL2 - revision: 1344f41b7b
[33/30120c] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[b9/5b27a7] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[99/9c3cf4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[56/ceea6e] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[fc/5a15e1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[52/9992ee] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[d2/e2aa17] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
[a0/c0283b] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR9984183)
[81/a3e342] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (ERR1160846)
[28/aa44c5] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (DRR028935)
[a1/90bc33] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (ERX1234253_ERR1160846)
[db/e542f2] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX6725035_SRR9984183)
[3b/731349] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (DRX026011_DRR028935)
[b4/d99391] Submitted process > SRA:SRA_TO_SAMPLESHEET
[32/580a50] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/74d134f23ad7be1592b6703d50788391/meta/mock.nf` [boring_bardeen] DSL2 - revision: 43c397a1ef
[4b/66b7ec] 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/4b/66b7ec5ceef0630424c492fa6b5b11

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:
View more details on GitHub Actions