diff --git a/nextflow.config b/nextflow.config index 9838500..2514745 100644 --- a/nextflow.config +++ b/nextflow.config @@ -169,7 +169,7 @@ profiles { // Script parameters params { - rootdir = "$VSC_DATA/spotless-benchmark" + rootdir = "$VSC_DATA_VO_USER/spotless-benchmark" outdir = [props: "${params.rootdir}/deconv_proportions", metrics: "${params.rootdir}/results", synthspot: "${params.rootdir}/synthetic_data/"] diff --git a/standards/standard.config b/standards/standard.config index 6d77180..d1d5e34 100644 --- a/standards/standard.config +++ b/standards/standard.config @@ -2,11 +2,11 @@ params { file_type = 'rds' // If there is a hyphen, we only run one scenario (and for sc_input only get number before hyphen) - // If there is no hyphen, run all eight scenarios at once + // If there is no hyphen, run all scenarios at once sc_input = (params.standard =~ /-/ ? "standards/reference/${params.standard.split('-')[0]}*.${params.file_type}" : "standards/reference/${params.standard}*.${params.file_type}") sp_input = (params.standard =~ /(-|gold)/ ? "standards/$params.standard/*.${params.file_type}" : - "standards/$params.standard-[0-9]/*.${params.file_type}") + "standards/$params.standard-*/*.${params.file_type}") annot = "celltype" sampleID = "none" skip_metrics = (file_type =~ /rds/ ? false : true) diff --git a/subworkflows/deconvolution/stride/run_method.nf b/subworkflows/deconvolution/stride/run_method.nf index b2d7cd2..34d8f49 100644 --- a/subworkflows/deconvolution/stride/run_method.nf +++ b/subworkflows/deconvolution/stride/run_method.nf @@ -1,6 +1,7 @@ process runSTRIDE { tag "stride_${sp_file_basename}" label "retry" + label "longer_time" container 'csangara/sp_stride:latest' echo true @@ -52,6 +53,7 @@ process runSTRIDE { process buildSTRIDEModel { tag "stride_build_$tag_suffix" label "retry" + label "longer_time" container 'csangara/sp_stride:latest' echo true