Commit 6d7f470b authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

replace '/work' in conf/test_genotoul_workq.config

parent 6f920d96
process.executor = 'slurm' process.executor = 'slurm'
includeConfig 'singularity.config' 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.queue = 'workq'
process { process {
......
...@@ -416,9 +416,12 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03 ...@@ -416,9 +416,12 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03
output: output:
file("nodes.dmp") into index_kaiju_nodes_final_ch 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 file("names.dmp") into index_kaiju_names_final_ch
/* when:
index_kaiju_db_final_ch.size() == 1*/
script: script:
""" """
wget ${database} wget ${database}
...@@ -435,7 +438,7 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03 ...@@ -435,7 +438,7 @@ if (!params.skip_kaiju && ('01_clean_qc' in step || '02_assembly' in step || '03
index_kaiju_nodes_final_ch = Channel index_kaiju_nodes_final_ch = Channel
.value(kaiju_Path + "/" + kaiju_Path_db + "/nodes.dmp") .value(kaiju_Path + "/" + kaiju_Path_db + "/nodes.dmp")
index_kaiju_db_final_ch = Channel 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 index_kaiju_names_final_ch = Channel
.value(kaiju_Path + "/" + kaiju_Path_db + "/names.dmp") .value(kaiju_Path + "/" + kaiju_Path_db + "/names.dmp")
} }
......
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