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Merge pull request #268 from replikation/freyja_integration
Freyja integration
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| process freyja { | ||
| label 'freyja' | ||
| errorStrategy 'retry' | ||
| maxRetries 1 | ||
| publishDir "${params.output}/${params.lineagedir}/${name}/lineage-proportion-by-reads", mode: 'copy', pattern: "*" | ||
|
|
||
| input: | ||
| tuple val(name), path(bam_file), path(reference) | ||
| output: | ||
| tuple val(name), path("*_freyja_aggregate.tsv"), emit: aggregate | ||
| tuple val(name), path("*_freyja_variants.tsv"), path("*_freyja_depths.tsv"), path("*_freyja_demix.tsv"), path("*_freyja_aggregate.tsv"), emit: fullresults | ||
| tuple val(name), path("*_freyja_plot.svg"), path("*_freyja_plot.png"), emit: plots, optional: true | ||
|
|
||
| script: | ||
| if ( params.freyja_update ) | ||
| { freyja_update_cmd = "mkdir data; freyja update --outdir data" | ||
| // here we will download the latest Freyja data again instead of using the files obtained when installing the conda env | ||
| freyja_ref_data = "data" | ||
| } | ||
| else | ||
| { freyja_update_cmd = " " | ||
| // this is the original path where inside of the container the Freyja data is stored | ||
| freyja_ref_data = "/opt/conda/envs/freyja-env/lib/python3.10/site-packages/freyja/data/" | ||
| } | ||
| """ | ||
| sed -i "s/^>.*\$/>MN908947.3/" ${reference} #rename reference-sequence as Alignment is done with this sequence-name even so using the same reference freyja will detect deviating names and throw an error | ||
| mkdir -p freyja_result/ | ||
| ${freyja_update_cmd} | ||
| freyja variants ${bam_file} \ | ||
| --variants ${name}_freyja_variants.tsv \ | ||
| --depths ${name}_freyja_depths.tsv \ | ||
| --ref ${reference} | ||
| freyja demix ${name}_freyja_variants.tsv \ | ||
| ${name}_freyja_depths.tsv \ | ||
| --output freyja_result/${name}_freyja_demix.tsv \ | ||
| --barcodes ${freyja_ref_data}/usher_barcodes.csv \ | ||
| --lineageyml ${freyja_ref_data}/lineages.yml | ||
| freyja aggregate freyja_result/ \ | ||
| --output ${name}_freyja_aggregate.tsv \ | ||
| freyja plot ${name}_freyja_aggregate.tsv \ | ||
| --output ${name}_freyja_plot.svg \ | ||
| --lineages \ | ||
| --mincov 10.0 #default minCoverage: 60 \ | ||
| --lineageyml ${freyja_ref_data}/lineages.yml | ||
| freyja plot ${name}_freyja_aggregate.tsv \ | ||
| --output ${name}_freyja_plot.png \ | ||
| --lineages \ | ||
| --mincov 10.0 #default minCoverage: 60 \ | ||
| --lineageyml ${freyja_ref_data}/lineages.yml | ||
| mv freyja_result/${name}_freyja_demix.tsv \$PWD #freyha_demix.tsv is put into a folder before to give it to freyja aggregate | ||
| """ | ||
| stub: | ||
| """ | ||
| touch stub_freyja_variants.tsv \ | ||
| stub_freyja_depths.tsv \ | ||
| stub_freyja_demix.tsv \ | ||
| stub_freyja_aggregate.tsv \ | ||
| stub_freyja_plot.png \ | ||
| stub_freyja_plot.svg | ||
| """ | ||
| } | ||
|
|
||
| process freyja_plot { | ||
| label 'freyja' | ||
| publishDir "${params.output}/${params.lineagedir}/", mode: 'copy', pattern: "*" | ||
|
|
||
| input: | ||
| path(aggregate_file) | ||
| output: | ||
| tuple path("*_freyja_plot.svg"), path("*_freyja_plot.png"), emit: results, optional: true | ||
|
|
||
| script: | ||
| """ | ||
| freyja plot ${aggregate_file} \ | ||
| --output combined_freyja_plot.svg \ | ||
| --lineages \ | ||
| --mincov 10.0 #default minCoverage: 60 | ||
| freyja plot ${aggregate_file} \ | ||
| --output combined_freyja_plot.png \ | ||
| --lineages \ | ||
| --mincov 10.0 #default minCoverage: 60 | ||
| """ | ||
| stub: | ||
| """ | ||
| touch stub_combined_freyja_plot.png \ | ||
| stub_combined_freyja_plot.svg | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -90,4 +90,8 @@ process lcs_plot { | |
| """ | ||
| lcs_bar_plot.R '${tsv}' ${cutoff} | ||
| """ | ||
| stub: | ||
| """ | ||
| touch stub.png | ||
| """ | ||
| } | ||
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