Commit 82d3c8d3 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

replace '/work' in conf/base.config

parent 6f920d96
process.executor = 'slurm'
includeConfig 'singularity.config'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /save -B /home -B /work/project -B /usr/local/bioinfo"
singularity.runOptions = "-B /work/bank/ -B /bank -B /work -B /work2 -B /save -B /home -B /work/project -B /usr/local/bioinfo"
process.queue = 'workq'
process {
......
......@@ -416,9 +416,12 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03
output:
file("nodes.dmp") into index_kaiju_nodes_final_ch
file("kaiju_db_refseq.fmi") into index_kaiju_db_final_ch
file("kaiju_db*.fmi") into index_kaiju_db_final_ch
file("names.dmp") into index_kaiju_names_final_ch
/* when:
index_kaiju_db_final_ch.size() == 1*/
script:
"""
wget ${database}
......@@ -435,7 +438,7 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03
index_kaiju_nodes_final_ch = Channel
.value(kaiju_Path + "/" + kaiju_Path_db + "/nodes.dmp")
index_kaiju_db_final_ch = Channel
.value(kaiju_Path + "/" + kaiju_Path_db + "/kaiju_db_refseq.fmi")
.value(kaiju_Path + "/" + kaiju_Path_db + "/kaiju_db*.fmi")
index_kaiju_names_final_ch = Channel
.value(kaiju_Path + "/" + kaiju_Path_db + "/names.dmp")
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment