upload stats in ftp

nextflow.config

@@ -47,6 +47,7 @@ params {
   jdbcUrl = "jdbc:mysql://${params.host}:${params.port}/${params.dbname}"
 
   ncbiBaseUrl="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/"
+  readme="${projectDir}/../data/README.txt"
   //production_ftp_dir= "/nfs/production/flicek/ensembl/production/ensemblftp/rapid-release/species/"
   production_ftp_dir= "/nfs/production/flicek/ensembl/genebuild/genebuild_virtual_user/test_fra/"
   project = 'ensembl'

pipelines/nextflow/modules/copy_output_to_ensembl_ftp.nf

@@ -30,16 +30,15 @@ process COPY_OUTPUT_TO_ENSEMBL_FTP {
     species=scientific_name.toLowerCase()
     gca_string = gca.toLowerCase().replaceAll(/\./, "v").replaceAll(/_/, "")
     publish_dir =scientific_name +'/'+gca+'/'+getMetaValue(dbname, "species.annotation_source")[0].meta_value.toString() 
+    statistics_files = "${params.outDir}/$publish_dir/statistics/*summary.txt"
     ftp_stats = "${params.production_ftp_dir}/$publish_dir/statistics" 
     ftp_path = "${params.production_ftp_dir}/$scientific_name"
     """
     sudo -u genebuild mkdir -p $ftp_stats; \
-    
-    sudo -u genebuild rsync -ahvW $summary_file $ftp_stats && rsync -avhc $summary_file $ftp_stats; \
+    sudo -u genebuild cp ${params.readme} $ftp_stats; 
+    sudo -u genebuild cp $statistics_files  $ftp_stats; \
     sudo -u genebuild chmod 775 $ftp_path/* -R;
     sudo -u genebuild chgrp ensemblftp $ftp_path/* -R;
     """
-    //sudo -u genebuild find #production_ftp_dir#/species/Urophycis_tenuis -user genebuild -exec chmod g+w {} \;
-    //sudo -u genebuild find "$ftp_path" -user genebuild -exec chmod g+w {} ; \
-    //sudo -u genebuild find "$ftp_path" -user genebuild -exec chgrp -R ensemblftp {} \;
+    //sudo -u genebuild rsync -ahvW $summary_file $ftp_stats && rsync -avhc $summary_file $ftp_stats; \
 }

pipelines/nextflow/modules/omark/omark_output.nf

@@ -21,8 +21,8 @@ include { getMetaValue } from '../utils.nf'
 process OMARK_OUTPUT {
     tag "omark_output:$gca"
     label 'default'
-    //publishDir "${params.outDir}/$publish_dir/statistics", mode: 'copy'
-    storeDir "${params.outDir}/$publish_dir/statistics"
+    publishDir "${params.outDir}/$publish_dir/statistics", mode: 'copy'
+    //storeDir "${params.outDir}/$publish_dir/statistics/"
 
     input:
     tuple val(gca), val(dbname), val(publish_dir), path(summary_file), val(omark_dir)
@@ -37,8 +37,8 @@ process OMARK_OUTPUT {
     gca_string = gca.toLowerCase().replaceAll(/\./, "v").replaceAll(/_/, "")
     //def summary_name = summary_file
     summary_name = [species, gca_string, "omark", "proteins_detailed_summary.txt"].join("_")
-    //summary_file= summary_name
-    omark_file = task.workDir.resolve(summary_name+'_'+summary_file)
+    summary_file= summary_name
+    //omark_file = task.workDir.resolve(summary_name+'_'+summary_file)
     //summary_file.renameTo(new File(summary_file.getParent(), summary_name))   "proteins_detailed_summary.txt"
     //"""
     //cp $summary_file $summary_name