Conflicting errors with "baseCommand" vs "arguments" usage

Question

[ionox0]

When I include all of my static arguments in the baseCommand section I get an IOError that the filename for the log file is too long. However, when I put some of these static arguments in the arguments section, then some of my inputs get placed before them, which breaks the command.

More specifically, this method:

baseCommand:
- /bin/java
- -Xmx20g
- -Djava.io.tmpdir=/scratch
- -jar
- GenomeAnalysisTK.jar
- -T
- FindCoveredIntervals

Causes this error:

  IOError: [Errno 36] File name too long: u'outputFolder/log/file:---home-johnsoni-Innovation--Pipeline-cwl_tools-gatk-FindCoveredIntervals.cwl_-java-jdk1.8.0_25-bin-java_--Xmx20g_--Djava.io.tmpdir=-scratch_--jar_-gatk-GenomeAnalysisTK--3.3--0-GenomeAnalysisTK.jar_--T_FindCoveredIntervals_4-4-jobbXTDK3000.log'

And this method:

baseCommand:
- /bin/java

arguments:
- -Xmx20g
- -Djava.io.tmpdir=/scratch
- -jar
- GenomeAnalysisTK.jar
- -T
- FindCoveredIntervals

Causes the arguments to be placed out of order:

/bin/sh \
    -c \
    '/bin/java' '-Xmx20g' '--input_file' 'outputDolder/tmpB0vftO/stg1b9976f0-2b5d-4eb9-bb1a-c11c15ef0d30/Sample_standard_RG_MD.bam' '--intervals' '14' '-Djava.io.tmpdir=/scratch' '-jar' '/gatk/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar' '-T' 'FindCoveredIntervals' '--coverage_threshold' '20' '--minBaseQuality' '20' '--minMappingQuality' '20' '--out' 'sample.fci.list' --read_filter FailsVendorQualityCheck -rf BadMate -rf UnmappedRead -rf BadCigar '--reference_sequence' '/hg19/Homo_sapiens_assembly19.fasta'
Unrecognized option: --input_file

Should I supply a large value for the position parameter for each of the inputs, or is there another way to get the arguments to come before all of the inputs?

Answer 1

[fiakhan88]

Hi there, Did you consider using "position" for each argument? If you specify position, the arguments will appear in order. Hope this helps.

[ionox0]

Thank you fiakhan, yes my current solution is to supply large values for the position arguments, but I was wondering if there was a cleaner solution for that