readqc not always specifying the correct output file

[aclum]

The issue is with this line

metaT_ReadsQC/rqcfilter.wdl

Line 240 in f866a63

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

I this is not deterministic so sometimes you end up with the correct file and sometimes you end up with the rRNA file.

For this run the file that should be input to assembly is 3.6 G
nmdcda@perlmutter:login02:/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/31b007af-e328-40a7-926c-47ccb1f4789a/call-qc/metaTReadsQC/5fcf96a7-c485-4675-8df6-76573a8c8c06/call-qc/execution/filtered> ls -lh *fastq.gz
-rw-rw-r--+ 2 nmjaws nmjaws 3.6G Aug 7 15:37 raw.anqrpht.fastq.gz
-rw-r--r--+ 11 nmjaws nmjaws 1.1G Aug 7 13:29 rRNA.fastq.gz

The finalize step the file size is the same for the rrna file and the clean file
(nersc-python) nmdcda@perlmutter:login02:/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/31b007af-e328-40a7-926c-47ccb1f4789a/call-qc/metaTReadsQC/5fcf96a7-c485-4675-8df6-76573a8c8c06/call-finish_rqc/execution> ls -lh *fastq.gz
-rw-r--r--+ 11 nmjaws nmjaws 1.1G Aug 7 13:29 Ga0491221_filtered.fastq.gz
-rw-r--r--+ 11 nmjaws nmjaws 1.1G Aug 7 13:29 Ga0491221_rRNA.fastq.gz

Please update the code to use a file suffix of 'anqrpht.fastq.gz' for the filtered output of task rqcfilter

[kaijli]

Created a branch, will merge when benchmark reruns confirmed good