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remove glob to select target filtered fastq file #37

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aclum opened this issue Aug 9, 2024 · 0 comments · Fixed by #36
Closed

remove glob to select target filtered fastq file #37

aclum opened this issue Aug 9, 2024 · 0 comments · Fixed by #36
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@kaijli

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@aclum
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aclum commented Aug 9, 2024

Explicity set a file suffix on

ReadsQC/shortReadsqc.wdl

Line 221 in 23075c8

File filtered = glob("filtered/*fastq.gz")[0]

There is only one file with this extension for metagenomes so not as urgent as fixing microbiomedata/metaT_ReadsQC#7 but taking the first element of the glob is not deterministic if there is more than one file.

cc @vlilanl
vlilanl added a commit that referenced this issue Aug 15, 2024
@vlilanl
Added update to task rqcfilter outputs to fix issue #37
e251bc4
@vlilanl vlilanl linked a pull request Aug 23, 2024 that will close this issue
#32 updating logic for reads qc #36
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vlilanl added a commit that referenced this issue Aug 23, 2024
@vlilanl
Merge pull request #36 from microbiomedata/32-update-logic
d0915ae 
#32 updating logic for reads qc and #37 remove glob
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#32 updating logic for reads qc microbiomedata/ReadsQC
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