diff --git a/conf/modules.config b/conf/modules.config index c61dfe1..5269c6b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,6 +18,7 @@ process { mode: params.publish_dir_mode ] ext.args = params.integration_method + ext.args2 = params.eula_agreement } withName: 'FIND_NN_CLUSTER' { diff --git a/modules/local/plotting.nf b/modules/local/plotting.nf index 7f5a3a6..6dbc3aa 100644 --- a/modules/local/plotting.nf +++ b/modules/local/plotting.nf @@ -15,7 +15,6 @@ process DISPLAY_REDUCTION { val resolutions val makeLoupe val integration_tool - val eula_agreement @@ -35,7 +34,8 @@ process DISPLAY_REDUCTION { } else { integration_method = "NULL" } - def args = task.ext.args1 ?: 'NULL' + def args = task.ext.args ?: '' + def eula_agreement = task.ext.args2 ?: 'NULL' """ pcMax=\$(grep -i -E "^PCs used" $validation_log | perl -pe "s/^PCs.*- //g") diff --git a/workflows/scscape.nf b/workflows/scscape.nf index 4dd3916..5679fbd 100644 --- a/workflows/scscape.nf +++ b/workflows/scscape.nf @@ -253,8 +253,7 @@ workflow SCSCAPE { ch_nn_clusters_w_log.map { it[1] }, params.resolutions, params.makeLoupe, - params.integration_method, - params.eula_agreement + params.integration_method ) //CUSTOM_DUMPSOFTWAREVERSIONS ( // ch_versions.unique().collectFile(name: 'collated_versions.yml')