# # Copyright (C) 2015 INRA # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . # [global] # uncomment and set if not in the PATH, should be version >= 4.4.3 #makeflow = /usr/bin/makeflow # batch system type: local, condor, sge, moab, cluster, wq, hadoop, mpi-queue batch_system_type = local # add these options to all batch submit files batch_options = # add these options to limit the number of jobs sumitted in parallel limit_submission = 100 # on which socket host should run the web server server_socket_host = 127.0.0.1 # on which socket port should run the web server server_socket_port = 8080 #server_socket_port = 8083 # protocol used to access web server (http|https) server_socket_protocol = https # date format date_format = %d/%m/%Y #optional : key for jflow server ssl configuration ssl_certificate = certificate.crt ssl_certificate_chain = certificate_chain.crt ssl_private_key = private_key.key [email] # if you want an email to be sent at the end of the workflow execution # set the smtp_server and the from_address values smtp_server = smtp_port = from_address = from_password = # uncomment and set if you want to use these values for all the workflow # these variables can be overloaded within the workflow implementation by # using self.set_to_address("address"), self.set_subject("subject"), # self.set_message("message") functions #to_address = #subject = #message = #Purge email configuration #if you want to use purge option, an email is sent #In purge email you can fix for an extention : # the minimal duration min_extension_duration = 1 year # the minimal size min_extension_size = 1 Tbite # the price for min_extension_duration * min_extension_size min_extension_price = 300 Euros # delay (in days) after sending an email to indicate that the data will be deleted delay_purge = 30 # the url where prices are defined url_extension_price = http://url.extention.prices [database] host = localhost user = typo3 passwd = typo3 dbname = typo3 [storage] # where should be written the log file log_file = /ng6.log #level of logs to display in log_file log_level = logging.DEBUG|logging.WARNING|logging.ERROR|... # Where should data be stored save_directory = /ng6 # Where should the pipelines write results, should be accessible # by all cluster nodes work_directory = /work # Where should the pipelines write temporary files, should be # accessible by all cluster nodes tmp_directory = /tmp # Configure different storage directory # and associate retention date or duration # # eg with a duration [space_default] dir_name=default retention_period=3 # # eg with a fix date [space_final] dir_name=directory retention_date=12/03/2021 [ui] # This must be an absolute path of a directory mounted and accessible by the server user_base_directory = /work/ # where could be find binaries [softwares] # uncomment and set if not in the PATH # # Global softwares # #cutadapt = /usr/bin/cutadapt #blastall = /usr/bin/blastall #formatdb = /usr/bin/formatdb #blastn = /usr/bin/blastn #blastx = /usr/bin/blastx #makeblastdb = /usr/bin/makeblastdb #bwa = /usr/bin/bwa #samtools = /usr/bin/samtools #ktImportBLAST = /usr/local/bin/ktImportBLAST #fastqc = /nosave/software/fastqc/current/fastqc #fastq_illumina_filter = /usr/bin/fastq_illumina_filter #CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar #MarkDuplicates = /usr/bin/MarkDuplicates.jar #mothur = /usr/bin/mothur #fastx_reverse_complement = /usr/bin/fastx_reverse_complement #STAR = /usr/bin/STAR #fastuniq = /usr/local/bin/fastuniq #javaPICARD = /tools/java/jre1.8.0_45/bin/java # workflow specific # # r454_qc #sfffile = /usr/bin/sfffile #runAssembly = /usr/bin/runAssembly # illumina_rnaseq #geneBody_coverage.py = /usr/local/bin/geneBody_coverage.py #infer_experiment.py = /usr/local/bin/infer_experiment.py #inner_distance.py = /usr/local/bin/inner_distance.py #junction_saturation.py = /usr/local/bin/junction_saturation.py #RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py #junction_annotation.py = /usr/local/bin/junction_annotation.py #NormalizeFasta.jar = /usr/local/bin/NormalizeFasta.jar # radseq #ustacks = /usr/local/bin/ustacks #cstacks = /usr/local/bin/cstacks # methylseq #trim_galore = /nosave/software/trim_galore #bismark = /nosave/software/bismark_v0.8.3/bismark #bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation #bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor #for rmdup samtools_old v 0.19 #samtools_old = /usr/bin/samtools # gene_diversity #framebot = /usr/bin/FrameBot.jar #usearch = /usr/bin/usearch #cdhit = /usr/bin/cd-hit #ktImportText = /usr/local/bin/ImportText.pl # pacbio_qc #fofnToSmrtpipeInput.py = $INSTALLDI/current/analysis/bin/fofnToSmrtpipeInput.py #smrtpipe = $INSTALLDIR/current/smrtcmds/bin/smrtpipe # Set cluster parameters of some components [components] #Bismark.batch_options = -pe parallel_smp 8 -q wflowq #BismarkMethylationExtractor.batch_options = -l mem=8G -l h_vmem=16G -q wflowq #BWA.batch_options = -q unlimitq #AlignmentStats.batch_options = -q unlimitq #ContaminationSearch.batch_options = -q unlimitq #Trim_porechop.batch_options = --mem=4G -p wflowq -t 30 #Trim_porechop.modules = compiler/gcc-7.2.0,bioinfo/Porechop-0.2.1 # Set workflows group [workflows] # download workflows DownloadArchive.group = download DownloadSymlink.group = download DownloadURL.group = download # run workflows AddRun.group = addrun GeneDiversity.group = addrun IlluminaDiversityQC.group = addrun IlluminaMatePair.group = addrun IlluminaQualityCheck.group = addrun RnaSeqQualityCheck.group = addrun Methylseq.group = addrun PacBioQualityCheck.group = addrun PhiXCheck.group = addrun R454QualityCheck.group = addrun [resources] typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip #phix_bwa = /bank/bwadb/phi.fa #ecoli_bwa = /bank/bwadb/ecoli536 #yeast_bwa = /bank/bwadb/yeast.nt [454_mids] MID1 = ACGAGTGCGT MID2 = ACGCTCGACA MID3 = AGACGCACTC MID4 = AGCACTGTAG MID5 = ATCAGACACG MID6 = ATATCGCGAG MID7 = CGTGTCTCTA MID8 = CTCGCGTGTC MID9 = TAGTATCAGC MID10 = TCTCTATGCG MID11 = TGATACGTCT MID12 = TACTGAGCTA MID13 = CATAGTAGTG MID14 = CGAGAGATAC MID15 = ATACGACGTA MID16 = TCACGTACTA MID17 = CGTCTAGTAC MID18 = TCTACGTAGC MID19 = TGTACTACTC MID20 = ACGACTACAG MID21 = CGTAGACTAG MID22 = TACGAGTATG MID23 = TACTCTCGTG MID24 = TAGAGACGAG MID25 = TCGTCGCTCG MID26 = ACATACGCGT MID27 = ACGCGAGTAT MID28 = ACTACTATGT MID29 = ACTGTACAGT MID30 = AGACTATACT MID31 = AGCGTCGTCT MID32 = AGTACGCTAT MID33 = ATAGAGTACT MID34 = CACGCTACGT MID35 = CAGTAGACGT MID36 = CGACGTGACT MID37 = TACACACACT MID38 = TACACGTGAT MID39 = TACAGATCGT MID40 = TACGCTGTCT MID41 = TAGTGTAGAT MID42 = TCGATCACGT MID43 = TCGCACTAGT MID44 = TCTAGCGACT MID45 = TCTATACTAT MID46 = TGACGTATGT MID47 = TGTGAGTAGT MID48 = ACAGTATATA MID49 = ACGCGATCGA MID50 = ACTAGCAGTA MID51 = AGCTCACGTA MID52 = AGTATACATA MID53 = AGTCGAGAGA MID54 = AGTGCTACGA MID55 = CGATCGTATA MID56 = CGCAGTACGA MID57 = CGCGTATACA MID58 = CGTACAGTCA MID59 = CGTACTCAGA MID60 = CTACGCTCTA MID61 = CTATAGCGTA MID62 = TACGTCATCA MID63 = TAGTCGCATA MID64 = TATATATACA MID65 = TATGCTAGTA MID66 = TCACGCGAGA MID67 = TCGATAGTGA MID68 = TCGCTGCGTA MID69 = TCTGACGTCA MID70 = TGAGTCAGTA MID71 = TGTAGTGTGA MID72 = TGTCACACGA MID73 = TGTCGTCGCA MID74 = ACACATACGC MID75 = ACAGTCGTGC MID76 = ACATGACGAC MID77 = ACGACAGCTC MID78 = ACGTCTCATC MID79 = ACTCATCTAC MID80 = ACTCGCGCAC MID81 = AGAGCGTCAC MID82 = AGCGACTAGC MID83 = AGTAGTGATC MID84 = AGTGACACAC MID85 = AGTGTATGTC MID86 = ATAGATAGAC MID87 = ATATAGTCGC MID88 = ATCTACTGAC MID89 = CACGTAGATC MID90 = CACGTGTCGC MID91 = CATACTCTAC MID92 = CGACACTATC MID93 = CGAGACGCGC MID94 = CGTATGCGAC MID95 = CGTCGATCTC MID96 = CTACGACTGC MID97 = CTAGTCACTC MID98 = CTCTACGCTC MID99 = CTGTACATAC MID100 = TAGACTGCAC MID101 = TAGCGCGCGC MID102 = TAGCTCTATC MID103 = TATAGACATC MID104 = TATGATACGC MID105 = TCACTCATAC MID106 = TCATCGAGTC MID107 = TCGAGCTCTC MID108 = TCGCAGACAC MID109 = TCTGTCTCGC MID110 = TGAGTGACGC MID111 = TGATGTGTAC MID112 = TGCTATAGAC MID113 = TGCTCGCTAC MID114 = ACGTGCAGCG MID115 = ACTCACAGAG MID116 = AGACTCAGCG MID117 = AGAGAGTGTG MID118 = AGCTATCGCG MID119 = AGTCTGACTG MID120 = AGTGAGCTCG MID121 = ATAGCTCTCG MID122 = ATCACGTGCG MID123 = ATCGTAGCAG MID124 = ATCGTCTGTG MID125 = ATGTACGATG MID126 = ATGTGTCTAG MID127 = CACACGATAG MID128 = CACTCGCACG MID129 = CAGACGTCTG MID130 = CAGTACTGCG MID131 = CGACAGCGAG MID132 = CGATCTGTCG MID133 = CGCGTGCTAG MID134 = CGCTCGAGTG MID135 = CGTGATGACG MID136 = CTATGTACAG MID137 = CTCGATATAG MID138 = CTCGCACGCG MID139 = CTGCGTCACG MID140 = CTGTGCGTCG MID141 = TAGCATACTG MID142 = TATACATGTG MID143 = TATCACTCAG MID144 = TATCTGATAG MID145 = TCGTGACATG MID146 = TCTGATCGAG MID147 = TGACATCTCG MID148 = TGAGCTAGAG MID149 = TGATAGAGCG MID150 = TGCGTGTGCG MID151 = TGCTAGTCAG MID152 = TGTATCACAG MID153 = TGTGCGCGTG RL1 = ACACGACGACT,AGTCGTGGTGT RL2 = ACACGTAGTAT,ATACTAGGTGT RL3 = ACACTACTCGT,ACGAGTGGTGT RL4 = ACGACACGTAT,ATACGTGGCGT RL5 = ACGAGTAGACT,AGTCTACGCGT RL6 = ACGCGTCTAGT,ACTAGAGGCGT RL7 = ACGTACACACT,AGTGTGTGCGT RL8 = ACGTACTGTGT,ACACAGTGCGT RL9 = ACGTAGATCGT,ACGATCTGCGT RL10 = ACTACGTCTCT,AGAGACGGAGT RL11 = ACTATACGAGT,ACTCGTAGAGT RL12 = ACTCGCGTCGT,ACGACGGGAGT RL13 = AGACTCGACGT,ACGTCGGGTCT RL14 = AGTACGAGAGT,ACTCTCGGACT RL15 = AGTACTACTAT,ATAGTAGGACT RL16 = AGTAGACGTCT,AGACGTCGACT RL17 = AGTCGTACACT,AGTGTAGGACT RL18 = AGTGTAGTAGT,ACTACTAGACT RL19 = ATAGTATACGT,ACGTATAGTAT RL20 = CAGTACGTACT,AGTACGTGCTG RL21 = CGACGACGCGT,ACGCGTGGTCG RL22 = CGACGAGTACT,AGTACTGGTCG RL23 = CGATACTACGT,ACGTAGTGTCG RL24 = CGTACGTCGAT,ATCGACGGACG RL25 = CTACTCGTAGT,ACTACGGGTAG RL26 = GTACAGTACGT,ACGTACGGTAC RL27 = GTCGTACGTAT,ATACGTAGGAC RL28 = GTGTACGACGT,ACGTCGTGCAC RL29 = ACACAGTGAGT,ACTCACGGTGT RL30 = ACACTCATACT,AGTATGGGTGT RL31 = ACAGACAGCGT,ACGCTGTGTGT RL32 = ACAGACTATAT,ATATAGTGTGT RL33 = ACAGAGACTCT,AGAGTCTGTGT RL34 = ACAGCTCGTGT,ACACGAGGTGT RL35 = ACAGTGTCGAT,ATCGACAGTGT RL36 = ACGAGCGCGCT,AGCGCGCGCGT RL37 = ACGATGAGTGT,ACACTCAGCGT RL38 = ACGCGAGAGAT,ATCTCTGGCGT RL39 = ACGCTCTCTCT,AGAGAGGGCGT RL40 = ACGTCGCTGAT,ATCAGCGGCGT RL41 = ACGTCTAGCAT,ATGCTAGGCGT RL42 = ACTAGTGATAT,ATATCACGAGT RL43 = ACTCACACTGT,ACAGTGGGAGT RL44 = ACTCACTAGCT,AGCTAGGGAGT RL45 = ACTCTATATAT,ATATATGGAGT RL46 = ACTGATCTCGT,ACGAGATGAGT RL47 = ACTGCTGTACT,AGTACAGGAGT RL48 = ACTGTAGCGCT,AGCGCTAGAGT RL49 = AGACACTCACT,AGTGAGGGTCT RL50 = AGACATATAGT,ACTATAGGTCT RL51 = AGACGTGATCT,AGATCAGGTCT RL52 = AGAGTACAGAT,ATCTGTAGTCT RL53 = AGAGTATCTCT,AGAGATAGTCT RL54 = AGATACGCTGT,ACAGCGTGTCT RL55 = AGATCTAGTCT,AGACTAGGTCT RL56 = AGCAGCGTAGT,ACTACGCGGCT RL57 = AGCGCACGAGT,ACTCGTGGGCT RL58 = AGCGTGTGCGT,ACGCACAGGCT RL59 = AGCTAGATACT,AGTATCTGGCT RL60 = AGCTGTCGACT,AGTCGACGGCT RL61 = AGTATGCACGT,ACGTGCAGACT RL62 = AGTCGCGCTAT,ATAGCGGGACT RL63 = AGTCTGTCTGT,ACAGACGGACT RL64 = ATACACACGAT,ATCGTGGGTAT RL65 = ATACGCGTGCT,AGCACGGGTAT RL66 = ATACTAGCACT,AGTGCTGGTAT RL67 = ATAGAGCTAGT,ACTAGCTGTAT RL68 = ATATAGAGTAT,ATACTCTGTAT RL69 = ATCGCTCACGT,ACGTGAGGGAT RL70 = ATCGTCAGTCT,AGACTGAGGAT RL71 = ATCTCTCGTAT,ATACGAGGGAT RL72 = ATCTGAGACGT,ACGTCTCGGAT RL73 = ATGCTACGTCT,AGACGTGGCAT RL74 = ATGTGACTACT,AGTAGTCGCAT RL75 = CACGAGACAGT,ACTGTCTGGTG RL76 = CACGCGAGTCT,AGACTCGGGTG RL77 = CACGCTACGAT,ATCGTAGGGTG RL78 = CACGTGTATAT,ATATACAGGTG RL79 = CACTACGATGT,ACATCGTGGTG RL80 = CACTATACTCT,AGAGTATGGTG RL81 = CAGCGTACTGT,ACAGTAGGCTG RL82 = CAGTCTCTAGT,ACTAGAGGCTG RL83 = CATAGTCGCGT,ACGCGACGATG RL84 = CGAGACACTAT,ATAGTGTGTCG RL85 = CGAGAGTGTGT,ACACACTGTCG RL86 = CGAGTCATCGT,ACGATGAGTCG RL87 = CGATCGTATAT,ATATACGGTCG RL88 = CGCAGTACGCT,AGCGTACGGCG RL89 = CGCGATCGTAT,ATACGATGGCG RL90 = CGCGCTATACT,AGTATAGGGCG RL91 = CGTACAGATAT,ATATCTGGACG RL92 = CGTAGCTCTCT,AGAGAGCGACG RL93 = CGTATAGTGCT,AGCACTAGACG RL94 = CGTCAGCGACT,AGTCGCGGACG RL95 = CGTCGCAGTGT,ACACTGGGACG RL96 = CGTCTCACGAT,ATCGTGGGACG RL97 = CGTGACTCAGT,ACTGAGTGACG RL98 = CTACACGCTCT,AGAGCGGGTAG RL99 = CTACGATATGT,ACATATGGTAG RL100 = CTAGACAGACT,AGTCTGTGTAG RL101 = CTAGTACTCAT,ATGAGTAGTAG RL102 = CTATATGTCGT,ACGACATGTAG RL103 = CTATCGACACT,AGTGTCGGTAG RL104 = CTATGTAGAGT,ACTCTACGTAG RL105 = CTCACGTACAT,ATGTACGGGAG RL106 = CTCGAGTCTCT,AGAGACTGGAG RL107 = CTCGTCGAGAT,ATCTCGAGGAG RL108 = CTCTACAGCGT,ACGCTGTGGAG RL109 = CTGTCGTGCGT,ACGCACGGCAG RL110 = CTGTGACGTGT,ACACGTCGCAG RL111 = GACGCTGTCGT,ACGACAGGGTC RL112 = GACGTATGACT,AGTCATAGGTC RL113 = GACTAGCTAGT,ACTAGCTGGTC RL114 = GAGACGTCGCT,AGCGACGGCTC RL115 = GAGAGAGACGT,ACGTCTCGCTC RL116 = GCGTAGACTAT,ATAGTCTGCGC RL117 = GCGTCGTGTCT,AGACACGGCGC RL118 = GCTCTCTACGT,ACGTAGGGAGC RL119 = GTACACTGTAT,ATACAGGGTAC RL120 = GTACGCGACAT,ATGTCGGGTAC RL121 = GTACTATAGAT,ATCTATGGTAC RL122 = GTACTGAGTCT,AGACTCGGTAC RL123 = GTAGCTAGCGT,ACGCTAGGTAC RL124 = GTAGTCACTGT,ACAGTGAGTAC RL125 = GTAGTGTCACT,AGTGACAGTAC RL126 = GTATACATAGT,ACTATGTGTAC RL127 = GTCATCGTCGT,ACGACGAGGAC RL128 = GTCGACACGCT,AGCGTGTGGAC RL129 = GTCGAGTGAGT,ACTCACTGGAC RL130 = GTCTACTATCT,AGATAGTGGAC RL131 = GTGTCTAGACT,AGTCTAGGCAC RL132 = GTGTGTATCGT,ACGATACGCAC