Mercurial > repos > rliterman > csp2
changeset 25:5c609acba34e
"planemo upload"
| author | rliterman |
|---|---|
| date | Tue, 03 Dec 2024 15:56:32 -0500 |
| parents | 75070dbe67b1 |
| children | 6f85641ecd48 |
| files | CSP2/subworkflows/fetchData/main.nf csp_screen.xml |
| diffstat | 2 files changed, 4 insertions(+), 0 deletions(-) [+] |
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--- a/CSP2/subworkflows/fetchData/main.nf Tue Dec 03 15:15:27 2024 -0500 +++ b/CSP2/subworkflows/fetchData/main.nf Tue Dec 03 15:56:32 2024 -0500 @@ -21,6 +21,8 @@ // Set SKESA cores to 4 or fewer skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer +println "params.cores: ${params.cores}" +println "skesa_cpus: ${skesa_cpus}" workflow { main:
--- a/csp_screen.xml Tue Dec 03 15:15:27 2024 -0500 +++ b/csp_screen.xml Tue Dec 03 15:56:32 2024 -0500 @@ -60,6 +60,7 @@ nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; zip -r work.zip work + zip -r csp2.zip CSP2_Screen_Output ]]> </command> <inputs> @@ -85,6 +86,7 @@ <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" /> <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> + <data name="out_dir" format="zip" label="CSP2 Directory" from_work_dir="csp2.zip" /> <data name="work_dir" format="zip" label="Nextflow Work Directory" from_work_dir="work.zip" /> </outputs> <tests>