Remove trimreaddescription from reformat.sh command in shortReadsqc.wdl

[samobermiller]

Action:
Remove trimreaddescription=t from reformat.sh command in the stage_interleave task of shortReadsqc.wdl (introduced in SRA PR #55 (line, ReadsQC v1.0.20, 11/3/25)).

Issue:
The parameter is removing pair information from headers (example: header should be @NB551228:6:H7FFKBGX5:4:23602:17332:3792 1:N:0:CTGAAGCT+AGGCTATA but instead @NB551228:6:H7FFKBGX5:4:23602:17332:3792) which is causing parsing errors.

Direct test passed:
local on cromwell via /global/cfs/cdirs/m3408/www/test_data/smalltest.R1.fastq.gz and /global/cfs/cdirs/m3408/www/test_data/smalltest.R2.fastq.gz. Output headers on filtered.fastq.gz contain pair information (ex @NS500756:11:H7FHCBGXH:1:11101:5478:9880 1:N:0:AGCGAGAT+GATACTGG).

Impact:
Only non-interleaved (paired) data goes through the impacted stage_interleave task. The Reads QC Interleave workflow in workflows.yaml was still using the interleave_rqcfilter.wdl instead of rqcfilter.wdl (and therefore shortReadsqc.wdl) until PR microbiomedata/nmdc_automation#688, at which point the ReadsQC version was also updated to v1.0.22. This means that only paired ReadsQC records run under v1.0.22 on (from ~4/2026 on) are affected.

Assessment of existing records:
The below mongo query was used to count the number of paired ReadsQC records run under each version number after 10/1/2025. Results pasted below, indicating only 13 records in affected version.

Resolution of problematic records in mongo:

• Apply changesheet for problematic records indicating failure reason
• Delete problematic records
• Reapply problematic records to allow list

{
  "_id": "v1.0.20",
  "count": 486
}
{
  "_id": "v1.0.18",
  "count": 19,
}
{
  "_id": "v1.0.24",
  "count": 13,
}

recent_noninterleaved_RQC.json

MongoDB workflows query

[
{
'$match': {
'type': 'nmdc:ReadQcAnalysis',
'ended_at_time': {
'$gte': '2025-10-01T00:00:00.000000+00:00'
},
'processing_institution': 'NMDC'
}
}, {
'$lookup': {
'from': 'data_object_set',
'localField': 'has_input',
'foreignField': 'id',
'as': 'input_do_set',
'pipeline': [
{
'$match': {
'data_object_type': {
'$in': [
'Metagenome Raw Read 2', 'Metagenome Raw Read 1'
]
}
}
}
]
}
}, {
'$match': {
'$expr': {
'$gte': [
{
'$size': '$input_do_set'
}, 2
]
}
}
}, {
'$group': {
'_id': '$version',
'count': {
'$sum': 1
},
'details': {
'$push': '$$ROOT'
}
}
}
]