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Merged
merged 2 commits into from
Jun 11, 2024
Merged

Don't force same KMCP mode for all database #493

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94812b3
Remove --kmcp_mode and bump KMCP version
jfy133 Jun 10, 2024
124a9c9
Actually include KMCP Profile
jfy133 Jun 10, 2024
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -17,8 +17,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

| Tool | Previous version | New version |
| ---- | ---------------- | ----------- |
| KMCP | 0.9.1 | 0.9.4 |

### `Deprecated`

- [#492](https://github.com/nf-core/taxprofiler/pull/492) Removed `--kmcp_mode` parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)

## v1.1.7 - Augmented Akita Patch [2024-04-25]

### `Added`
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1 change: 0 additions & 1 deletion conf/test.config
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Expand Up @@ -42,7 +42,6 @@ params {
run_ganon = true
run_krona = true
run_kmcp = true
kmcp_mode = 0
krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
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1 change: 0 additions & 1 deletion conf/test_adapterremoval.config
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Expand Up @@ -41,7 +41,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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1 change: 0 additions & 1 deletion conf/test_bbduk.config
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Expand Up @@ -41,7 +41,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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1 change: 0 additions & 1 deletion conf/test_falco.config
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Expand Up @@ -41,7 +41,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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1 change: 0 additions & 1 deletion conf/test_fastp.config
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Expand Up @@ -42,7 +42,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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1 change: 0 additions & 1 deletion conf/test_krakenuniq.config
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Expand Up @@ -44,7 +44,6 @@ params {
run_krakenuniq = true
run_motus = false
run_kmcp = false
kmcp_mode = 0
run_ganon = false
run_krona = true
krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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1 change: 0 additions & 1 deletion conf/test_malt.config
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Expand Up @@ -44,7 +44,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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1 change: 0 additions & 1 deletion conf/test_motus.config
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Expand Up @@ -43,7 +43,6 @@ params {
run_krakenuniq = false
run_motus = true
run_kmcp = false
kmcp_mode = 0
run_ganon = false
motus_save_mgc_read_counts = false
motus_remove_ncbi_ids = false
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1 change: 0 additions & 1 deletion conf/test_nopreprocessing.config
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Expand Up @@ -39,7 +39,6 @@ params {
run_krakenuniq = true
run_motus = false
run_kmcp = true
kmcp_mode = 0
run_ganon = true
run_krona = true
}
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1 change: 0 additions & 1 deletion conf/test_noprofiling.config
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Expand Up @@ -40,7 +40,6 @@ params {
run_krakenuniq = false
run_motus = false
run_kmcp = false
kmcp_mode = 0
run_ganon = false
}

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1 change: 0 additions & 1 deletion conf/test_nothing.config
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Expand Up @@ -39,7 +39,6 @@ params {
run_krakenuniq = false
run_motus = false
run_kmcp = false
kmcp_mode = 0
run_ganon = false
}

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1 change: 0 additions & 1 deletion conf/test_prinseqplusplus.config
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Expand Up @@ -41,7 +41,6 @@ params {
run_motus = false
run_ganon = false
run_kmcp = false
kmcp_mode = 0
}

process {
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