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Fix --skip_busco #256

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Merged
merged 9 commits into from
Nov 23, 2021
Merged

Fix --skip_busco #256

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d548ea7
fix-skip_busco
d4straub Nov 22, 2021
5c511e1
update changelog
d4straub Nov 22, 2021
82a1c86
fix channel
d4straub Nov 22, 2021
b131da1
update changelog
d4straub Nov 22, 2021
7f6bc44
Merge branch 'dev' of https://github.com/nf-core/mag into fix-skip_busco
d4straub Nov 22, 2021
2db3c2d
fix update changelog
d4straub Nov 22, 2021
a7f7e9d
merge upstream
d4straub Nov 23, 2021
a9399df
change gtdb default to mirror
d4straub Nov 23, 2021
b45414b
Update lib/WorkflowMag.groovy
d4straub Nov 23, 2021
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -19,9 +19,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#251](https://github.com/nf-core/mag/issus/251) - Update gtdbtk conda channel.
- [#256](https://github.com/nf-core/mag/pull/256) - Fix `--skip_busco`.
- [#236](https://github.com/nf-core/mag/pull/236) - Fix large assemblies (> 4 billion nucleotides in length).
- [#253](https://github.com/nf-core/mag/issues/253) - Fix MetaBAT2 error with nextflow version 21.10.x (21.04.03 is the latest functional version for nf-core/mag 2.1.0).
- [#254](https://github.com/nf-core/mag/pull/254) - Fix MetaBAT2 error with nextflow version 21.10.x (21.04.03 is the latest functional version for nf-core/mag 2.1.0).
- [#255](https://github.com/nf-core/mag/pull/255) - Update gtdbtk conda channel.
- [#258](https://github.com/nf-core/mag/pull/258) - FastP results are now in MultiQC.

## v2.1.0 - 2021/07/29
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3 changes: 1 addition & 2 deletions conf/test_hybrid_host_rm.config
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Expand Up @@ -24,6 +24,5 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.hybrid_host_rm.csv'
min_length_unbinned_contigs = 1
max_unbinned_contigs = 2
busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
gtdb = false
skip_busco = true
}
3 changes: 1 addition & 2 deletions lib/WorkflowMag.groovy
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Expand Up @@ -104,8 +104,7 @@ class WorkflowMag {
}

if (params.skip_busco && params.gtdb) {
log.error "Invalid combination of parameters --skip_busco and --gtdb are specififed! GTDB-tk bin classification requires bin filtering based on BUSCO QC results to avoid GTDB-tk errors."
System.exit(1)
log.warn "--skip_busco and --gtdb are specififed! GTDB-tk will be omitted! Because GTDB-tk bin classification requires bin filtering based on BUSCO QC results to avoid GTDB-tk errors."
}

// Check if CAT parameters are valid
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -50,7 +50,7 @@ params {
cat_db = null
cat_db_generate = false
save_cat_db = false
gtdb = "https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz"
gtdb = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz"
gtdbtk_min_completeness = 50.0
gtdbtk_max_contamination = 10.0
gtdbtk_min_perc_aa = 10
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9 changes: 5 additions & 4 deletions workflows/mag.nf
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Expand Up @@ -183,9 +183,10 @@ if (!params.keep_lambda) {
.set { ch_nanolyse_db }
}

if (params.gtdb) {
gtdb = params.skip_busco ? false : params.gtdb
if (gtdb) {
Channel
.value(file( "${params.gtdb}" ))
.value(file( "${gtdb}" ))
.set { ch_gtdb }
} else {
ch_gtdb = Channel.empty()
Expand Down Expand Up @@ -549,7 +550,7 @@ workflow MAG {
* GTDB-tk: taxonomic classifications using GTDB reference
*/
ch_gtdbtk_summary = Channel.empty()
if ( params.gtdb ){
if ( gtdb ){
GTDBTK (
METABAT2_BINNING.out.bins,
ch_busco_summary,
Expand All @@ -559,7 +560,7 @@ workflow MAG {
ch_gtdbtk_summary = GTDBTK.out.summary
}

if (!params.skip_busco || !params.skip_quast || params.gtdb){
if (!params.skip_busco || !params.skip_quast || gtdb){
BIN_SUMMARY (
METABAT2_BINNING.out.depths_summary,
ch_busco_summary.ifEmpty([]),
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