snap fails on files without an fq/fa suffix

[camillescott]

Running the following command:

transrate --assembly _work/lamp10.fasta --left _work/brain_paired.qc.fq.gz.keep.keep.abundfilt.1.fq --right _work/brain_paired.qc.fq.gz.keep.keep.abundfilt.2.fq --threads 16 --reference _work/danRer.pep.fa --output _work/lamp10.fasta.transrate-test

Results in the run failing, and the following error output:

[ERROR] 2015-07-14 00:14:32 : Version Info: This is the most recent version of Salmon.
# salmon (alignment-based) v0.4.2
# [ program ] => salmon 
# [ command ] => quant 
# [ libType ] => { IU }
# [ alignments ] => { /mnt/lustre_scratch_2012/camille/2015-petMarSB/_work/lamp10.fasta.transrate-test/lamp10/brain_paired.qc.fq.gz.keep.keep.abundfilt.1.brain_paired.qc.fq.gz.keep.keep.abundfilt.2.lamp10.bam }
# [ targets ] => { /mnt/lustre_scratch_2012/camille/2015-petMarSB/_work/lamp10.fasta }
# [ threads ] => { 16 }
# [ sampleOut ] => { }
# [ sampleUnaligned ] => { }
# [ output ] => { . }
# [ useVBOpt ] => { }
# [ useErrorModel ] => { }
============
Exception : [The provided alignment file: "/mnt/lustre_scratch_2012/camille/2015-petMarSB/_work/lamp10.fasta.transrate-test/lamp10/brain_paired.qc.fq.gz.keep.keep.abundfilt.1.brain_paired.qc.fq.gz.keep.keep.abundfilt.2.lamp10.bam" does not exist!
]
============
/mnt/home/welcherc/bin/bin/salmon alignment-quant was invoked improperly.
For usage information, try /mnt/home/welcherc/bin/bin/salmon quant --help-alignments
Exiting.

[ERROR] 2015-07-14 00:14:32 : Salmon failed

The issue appears to be that SNAP doesn't accept files which don't have an .fa or .fq extension, which seems to me to be a common occurrence. Adding the extensions fixes the problem. Would it be possible / desirable to modify SNAP's invocation to fix extensions with soft linking or to pass in a filetype argument?

[macmanes]

+1 on needing a fix here. Given khmer split-reads script appends .1 and .2 to the filename by default, which breaks SNAP, this is annoying. SNAP says you can specify filetype using the -fastq flag. Why not just add this - using transrate this is the only thing people should be passing anyway..

[blahah]

Seems sensible :)

[AlesBucek]

I'm wondering, is there already a fix for this issue?