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Refactor ext config as params #308

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Update modules/local/aspera_cli/main.nf

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Closed

Refactor ext config as params #308

Update modules/local/aspera_cli/main.nf
c67f91a
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GitHub Actions / JUnit Test Report failed May 1, 2024 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

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: 

assert workflow.success
       |        |
       workflow false
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.03.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/9a9a9677f4ce0035e7db385bc0d084c/meta/mock.nf` [crazy_stonebraker] DSL2 - revision: 939c98e37e
Downloading plugin [email protected]
[6c/7d0657] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[63/b8dc38] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[53/484645] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[35/5c45f7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
WARN: Process `SRA:SRA_RUNINFO_TO_FTP` publishDir path contains a variable with a null value
[74/2043a7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
WARN: Process `SRA:SRA_RUNINFO_TO_FTP` publishDir path contains a variable with a null value
[c5/26404b] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[ae/c5065f] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
WARN: Process `SRA:ASPERA_CLI` publishDir path contains a variable with a null value
[7e/5c428f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
WARN: Process `SRA:ASPERA_CLI` publishDir path contains a variable with a null value
[76/c673e8] Submitted process > SRA:SRA_TO_SAMPLESHEET (SRX6725035_SRR9984183)
WARN: Process `SRA:SRA_RUNINFO_TO_FTP` publishDir path contains a variable with a null value
[5b/41fd07] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
WARN: Process `SRA:ASPERA_CLI` publishDir path contains a variable with a null value
WARN: Process `SRA:ASPERA_CLI` publishDir path contains a variable with a null value
[b1/4195c8] Submitted process > SRA:SRA_TO_SAMPLESHEET (ERX1234253_ERR1160846)
ERROR ~ Error executing process > 'SRA:ASPERA_CLI (DRX026011_DRR028935)'

Caused by:
  Process `SRA:ASPERA_CLI (DRX026011_DRR028935)` terminated with an error exit status (1)

Command executed:

  ascp \
      -QT -l 300m -P33001 \
      -i $CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \
      [email protected]:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz \
      DRX026011_DRR028935_1.fastq.gz
  
  echo "cc01df82a9354bb6b3be93483b20c35a  DRX026011_DRR028935_1.fastq.gz" > DRX026011_DRR028935_1.fastq.gz.md5
  md5sum -c DRX026011_DRR028935_1.fastq.gz.md5
  
  ascp \
      -QT -l 300m -P33001 \
      -i $CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \
      [email protected]:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz \
      DRX026011_DRR028935_2.fastq.gz
  
  echo "941c9998d746416dad53c94c480ddf30  DRX026011_DRR028935_2.fastq.gz" > DRX026011_DRR028935_2.fastq.gz.md5
  md5sum -c DRX026011_DRR028935_2.fastq.gz.md5
  
  cat <<-END_VERSIONS > versions.yml
  "SRA:ASPERA_CLI":
      aspera_cli: $(ascli --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  
  Session Stop  (Error: Client unable to connect to server (check UDP port and firewall))

Command error:
  Unable to find image 'quay.io/biocontainers/aspera-cli:4.14.0--hdfd78af_1' locally
  4.14.0--hdfd78af_1: Pulling from biocontainers/aspera-cli
  642efca944a0: Already exists
  bd9ddc54bea9: Pulling fs layer
  7b8e1e5ce0be: Pulling fs layer
  bd9ddc54bea9: Download complete
  bd9ddc54bea9: Pull complete
  7b8e1e5ce0be: Verifying Checksum
  7b8e1e5ce0be: Download complete
  7b8e1e5ce0be: Pull complete
  Digest: sha256:07678dfe3a66d095861841dd147739d0acdfe4b96fca339d68acb3050f12aac2
  Status: Downloaded newer image for quay.io/biocontainers/aspera-cli:4.14.0--hdfd78af_1
  
  Session Stop  (Error: Client unable to connect to server (check UDP port and firewall))

Work dir:
  /home/runner/work/fetchngs/fetchngs/~/tests/9a9a9677f4ce0035e7db385bc0d084c/work/ae/c5065f3e0ee93445bc120e6bdaee9f

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/fetchngs/fetchngs/~/tests/9a9a9677f4ce0035e7db385bc0d084c/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
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