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Try adding nextflow strict #461

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merged 16 commits into from
Apr 4, 2024
Merged

Try adding nextflow strict #461

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4d6e111
Try adding nextflow strict
jfy133 Mar 21, 2024
aaf6d62
Start fixing untar MALT db error
jfy133 Mar 21, 2024
d8f136d
Optimise database untarring and prevent publishing clashses
jfy133 Mar 21, 2024
c099269
Update changelog
jfy133 Mar 21, 2024
28c250e
Update changelog
jfy133 Mar 21, 2024
c5b112d
Add nf-validation specific parameter to ignore list
jfy133 Mar 21, 2024
06d7ecf
Remove a debugging dump
jfy133 Mar 22, 2024
b527a85
Remove final dump
jfy133 Mar 22, 2024
e6097e6
Actually remove it
jfy133 Mar 22, 2024
4dc0900
Fix occasional split errors, due to db_params replacement not actuall…
jfy133 Mar 28, 2024
630a25c
Update workflows/taxprofiler.nf
jfy133 Mar 28, 2024
1b4c5f0
Add option to save uncompressed databases, turn
jfy133 Apr 4, 2024
54a6cd7
Apply suggestions from code review
jfy133 Apr 4, 2024
968ae64
[automated] Fix code linting
nf-core-bot Apr 4, 2024
f894a4b
Update CHANGELOG.md
jfy133 Apr 4, 2024
2ebce4c
Update nextflow_schema.json
jfy133 Apr 4, 2024
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14 changes: 6 additions & 8 deletions workflows/taxprofiler.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -179,14 +179,12 @@ workflow TAXPROFILER {
}
.transpose(by: 0)

ch_final_dbs = ch_dbs_for_untar.skip.mix( ch_outputdb_from_untar )
ch_final_dbs
.map { db_meta, db -> [ db_meta.db_params ]
def corrected_db_params = db_meta.db_params == null ? '' : db_meta.db_params
db_meta.db_params = corrected_db_params
[ db_meta, db ]
}

ch_final_dbs = ch_dbs_for_untar.skip
.mix( ch_outputdb_from_untar )
.map { db_meta, db ->
def corrected_db_params = db_meta.db_params == null ? [ db_params: '' ] : [ db_params: db_meta.db_params ]
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[ db_meta + corrected_db_params, db ]
}

/*
MODULE: Run FastQC
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