Rfam library files - Githubissues

Hello,

First of all - thank you, @mr-c, for the response to my previous problem!

I've been further trying to run emg workflows, specifically emg-pipeline-v4-paired.cwl, on my machine. I have run into several more issues, most of which seem too trivial to formulate as formal issues. If there is a preferred channel of communication, please, let me know.

Some of the problems might reveal my unfamiliarity with CWL, so I apologise, and I'm working on it! Seems like it's really quite an elegant way to deal with patchworks of wildly different tools, commonly known as pipelines.

Here's what I had problems with so far:

[ ] 1

ISSUE:

workflows/emg-pipeline-v4-paired-job.yaml specifies Rfam libraries contained within directories: "other" (e.g. .../CWL/data/libraries/Rfam/other/Archaea_SRP.cm), "ribosomal" (e.g. .../CWL/data/libraries/Rfam/ribosomal/RF02542.cm). I downloaded the Rfam database from ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.tar.gz, and it does not contain a corresponding directory structure.

SOLUTION: I have not found any so far.

[ ] 2

ISSUE:

MGRAST_base.py script used in tools/qc-stats.cwl is missing, can't find it online.

[ ] 3

ISSUE: At step trim_quality_control when running workflows/emg-qc-paired.cwl:

[job trim_quality_control] /tmp/tmp688nyarp$ /bin/sh \
    -c \
    'java' 'org.usadellab.trimmomatic.Trimmomatic' 'PE' '-trimlog' 'trim.log' '-threads' '8' '-phred33' '/tmp/tmpvkjt1pef/stg827d3176-4f1b-4179-8404-4b46397fff43/merged_with_unmerged_reads' 'merged_with_unmerged_reads.trimmed.fastq' 'LEADING:3' 'TRAILING:3' 'SLIDINGWINDOW:4:15' 'MINLEN:100'
Error: Could not find or load main class org.usadellab.trimmomatic.Trimmomatic

EXPLANATION: On my computer / a different version of Trimmomatic installs as a bash executable, which then calls java.

SOLUTION: change: baseCommand [ java, org.usadellab.trimmomatic.Trimmomatic ] to: baseCommand [ trimmomatic ]

[ ] 4

ISSUE: Is Trimmomatic output log file saved in a directory when it can be found?

Error collecting output for parameter 'output_log':
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3: Traceback (most recent call last):
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3: 
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3:   File "/P/cwl/venv/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 707, in collect_output
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3:     raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3: 
ebi-metagenomics-cwl/tools/trimmomatic.cwl:221:3: cwltool.errors.WorkflowException: Did not find output file with glob pattern: '['trim.log']'

SOLUTION: For now, I just commented out the output_log section of outputs in trimmomatic.cwl (lines 221-233). Guess that might break something, I'm sure there's a better solution.

EBI-Metagenomics / ebi-metagenomics-cwl

Rfam library files #78