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input_simple.yaml
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input_simple.yaml
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# pipeline data files
16s_blastdb_dir:
class: Directory
location: input/16S_rRNA
23s_blastdb_dir:
class: Directory
location: input/23S_rRNA
5s_model_path:
class: File
location: input/RF00001.cm
AntiFamLib:
class: Directory
location: input/AntiFamLib
asn2pas_xsl:
class: File
location: input/asn2pas.xsl
blast_rules_db_dir:
class: Directory
location: input/uniColl_path/blast_dir
CDDdata: # ${GP_HOME}/third-party/data/CDD/cdd - this is rpsblastdb
class: Directory
location: input/CDD
CDDdata2: # ${GP_HOME}/third-party/data/cdd_add
class: Directory
location: input/cdd_add
defline_cleanup_rules: # defline_cleanup_rules # ${GP_HOME}/etc/product_rules.prt
class: File
location: input/product_rules.prt
gene_master_ini:
class: File
location: input/gene_master.ini
genemark_path:
class: Directory
location: input/GeneMark
hmm_path:
class: Directory
location: input/uniColl_path/real_hmms
hmms_tab:
class: File
location: input/uniColl_path/real_hmms.tab
naming_blast_db: # NamingDatabase
class: Directory
location: input/uniColl_path/blast_dir # this one might have created problems for assign_cluster, let's try this:
naming_hmms_combined: # ${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming_hmms_combined.mft
class: Directory
location: input/uniColl_path/naming_hmms
naming_hmms_tab:
class: File
location: input/uniColl_path/naming_hmms.tab
naming_sqlite: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming.sqlite
class: File
location: input/uniColl_path/naming.sqlite
rfam_amendments:
class: File
location: input/rfam-amendments.xml
rfam_model_path:
class: File
location: input/Rfam.selected1.cm
rfam_stockholm:
class: File
location: input/Rfam.seed
selenoproteins: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/Selenoproteins/selenoproteins, it's blastdb
class: Directory
location: input/selenoproteins
taxon_db:
class: File
location: input/uniColl_path/taxonomy.sqlite3
thresholds:
class: File
location: input/thresholds.xml
uniColl_cache:
class: Directory
location: input/uniColl_path/cache
#uniColl_path:
# class: Directory
# location: input/uniColl_path
univ_prot_xml:
class: File
location: input/uniColl_path/universal.xml
val_res_den_xml:
class: File
location: input/validation-results.xml
wp_hashes:
class: File
location: input/uniColl_path/wp-hashes.sqlite
#
# Setup for template prepartion
#
submit_block_template_static:
class: File
location: input_template/submit_block_static.template
molinfo_complete_asn:
class: File
location: input_template/molinfo_complete.asn
molinfo_wgs_asn:
class: File
location: input_template/molinfo_wgs.asn