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replace local/medaca with nf-core/medaka and add busco output to multiqc #310

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replace local/medaca with nf-core/medaka and add busco output to multiqc #310

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8 changes: 8 additions & 0 deletions assets/multiqc_config_hybrid.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ run_modules:
- pycoqc
- kraken2
- quast
- busco
- prokka
- bakta

Expand Down Expand Up @@ -63,6 +64,11 @@ module_order:
info: "This section of the report shows Quast QC results for assembled genomes with Unicycler."
path_filters:
- "./quast/*/report.tsv"
- busco:
name: "ASSEMBLY QC: BUSCO"
info: "This section of the report shows BUSCO completeness results for assembled genomes."
path_filters:
- "./busco/*"
- prokka:
name: "ANNOTATION: Prokka"
info: "This section of the report shows Prokka annotation results for reads after adapter trimming and quality trimming."
Expand All @@ -87,6 +93,8 @@ report_section_order:
after: general_stats
quast:
after: general_stats
busco:
after: quast
prokka:
before: nf-core-bacass-methods-description
bakta:
Expand Down
8 changes: 8 additions & 0 deletions assets/multiqc_config_long.yml
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Expand Up @@ -14,6 +14,7 @@ run_modules:
- pycoqc
- kraken2
- quast
- busco
- prokka
- bakta

Expand Down Expand Up @@ -46,6 +47,11 @@ module_order:
info: "This section of the report shows Quast QC results for assembled genomes with Unicycler."
path_filters:
- "./quast/*/report.tsv"
- busco:
name: "ASSEMBLY QC: BUSCO"
info: "This section of the report shows BUSCO completeness results for assembled genomes."
path_filters:
- "./busco/*"
- prokka:
name: "ANNOTATION: Prokka"
info: "This section of the report shows Prokka annotation results for reads after adapter trimming and quality trimming."
Expand All @@ -66,6 +72,8 @@ report_section_order:
after: general_stats
quast:
after: general_stats
busco:
after: quast
prokka:
before: nf-core-bacass-methods-description
bakta:
Expand Down
8 changes: 8 additions & 0 deletions assets/multiqc_config_short.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ run_modules:
- fastp
- kraken2
- quast
- busco
- prokka
- bakta

Expand Down Expand Up @@ -45,6 +46,11 @@ module_order:
info: "This section of the report shows Quast QC results for assembled genomes with Unicycler."
path_filters:
- "./quast/*/report.tsv"
- busco:
name: "ASSEMBLY QC: BUSCO"
info: "This section of the report shows BUSCO completeness results for assembled genomes."
path_filters:
- "./busco/*"
- prokka:
name: "ANNOTATION: Prokka"
info: "This section of the report shows Prokka annotation results for reads after adapter trimming and quality trimming."
Expand All @@ -65,6 +71,8 @@ report_section_order:
after: general_stats
quast:
after: general_stats
busco:
after: quast
prokka:
before: nf-core-bacass-methods-description
bakta:
Expand Down
1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -248,6 +248,7 @@ process {

withName: 'MEDAKA' {
ext.args = ''
ext.prefix = { "${meta.id}_polished_genome" }
publishDir = [
path: { "${params.outdir}/Medaka" },
mode: params.publish_dir_mode,
Expand Down
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