only keep metadata in references.json

bin/update_references.lua

@@ -322,7 +322,8 @@ for name, values in pairs(refs.species) do
   if file_exists(name .. "/annotation_preclean.gff3") then
     os.remove(name .. "/annotation_preclean.gff3")
   end
-  values.gff = lfs.currentdir() .. "/" .. name .. "/annotation.gff3"
+  values.gff = nil -- lfs.currentdir() .. "/" .. name .. "/annotation.gff3"
+  out_stream = nil -- trigger GC -> trigger finishing of output file
 
   -- prepare genome FASTA
   if file_exists(values.genome) then
@@ -343,21 +344,24 @@ for name, values in pairs(refs.species) do
       end
     end
   end
-  values.genome = lfs.currentdir() .. "/" .. name .. "/genome.fasta"
-  values.chromosomes = lfs.currentdir() .. "/" .. name .. "/chromosomes.fasta"
+  values.genome = nil -- lfs.currentdir() .. "/" .. name .. "/genome.fasta"
+  values.chromosomes = nil -- lfs.currentdir() .. "/" .. name .. "/chromosomes.fasta"
 
   -- prepare GAF
   if file_exists(values.gaf) then
     os.execute("cp " .. values.gaf .. " " .. name .. "/go.gaf")
   end
-  values.gaf = lfs.currentdir() .. "/" .. name .. "/go.gaf"
+  values.gaf = nil -- lfs.currentdir() .. "/" .. name .. "/go.gaf"
 
   -- prepare models
   -- SNAP
   if values.snap_model and file_exists(values.snap_model) then
     os.execute("cp " .. values.snap_model .. " " .. name .. "/snap.hmm")
-    values.snap_model = lfs.currentdir() .. "/" .. name .. "/snap.hmm"
+    values.snap_model = true -- lfs.currentdir() .. "/" .. name .. "/snap.hmm"
+  else
+    values.snap_model = nil
   end
+
   -- AUGUSTUS
   AUG_MODEL_FILES = {'_parameters.cfg', '_parameters.cfg.orig1'}
   if values.augustus_model and file_exists(values.augustus_model) then
@@ -369,32 +373,34 @@ for name, values in pairs(refs.species) do
                .. lfs.currentdir() .. "/" ..name .. "/model")
     os.execute("cp -pr " .. gt.script_dir .. "/../data/augustus/profile "
                .. lfs.currentdir() .. "/" ..name .. "/profile")
-    values.augustus_model = lfs.currentdir() .. "/"
-                             .. name .. "/species/augustus_species"
-    for file in lfs.dir(values.augustus_model) do
+    values.augustus_model = true
+    local species_path = lfs.currentdir() .. "/" .. name .. "/species/augustus_species"
+    for file in lfs.dir(species_path) do
       --file is the current file or directory name
       for _,pat in ipairs(AUG_MODEL_FILES) do
         if file:match(pat .. "$") then
-          os.rename(values.augustus_model .."/" .. file,
-                    values.augustus_model .. "/augustus_species" .. pat)
+          os.rename(species_path .."/" .. file,
+                    species_path .. "/augustus_species" .. pat)
         end
       end
     end
+  else
+    values.augustus_model = nil
   end
 
   -- extract proteins
   -- XXX TODO: check for applicability of mapping
   os.execute("gt extractfeat -type CDS -join -retainids -translate -seqfile "
-    .. name .. "/genome.fasta -matchdescstart "
-    .. name .. "/annotation.gff3 > " .. name .. "/proteins_preclean.fasta")
+    .. name .. "/genome.fasta -matchdescstart -o ".. name .. "/proteins_preclean.fasta "
+    .. name .. "/annotation.gff3")
 
   -- open ggfile
   local ggfile = io.open(name .. "/ggline.gg", "w+")
   ggfile:write(name .. ": ")
 
   -- truncate proteins, make gg line
   if file_exists(name .. "/proteins_preclean.fasta") then
-    local keys, seqs =get_fasta_nosep(name .. "/proteins_preclean.fasta")
+    local keys, seqs = get_fasta_nosep(name .. "/proteins_preclean.fasta")
     local outfile = io.open(name .. "/proteins.fasta", "w+")
     for hdr, seq in pairs(seqs) do
       local trans_id = hdr:split(' ')[1]
@@ -405,9 +411,9 @@ for name, values in pairs(refs.species) do
   end
   ggfile:write("\n")
   if file_exists(name .. "/proteins_preclean.fasta") then
-    os.remove(name .. "/proteins_preclean.fasta")
+    --os.remove(name .. "/proteins_preclean.fasta")
   end
-  values.pep =lfs.currentdir() .. "/" .. name .. "/proteins.fasta"
+  values.pep = nil -- lfs.currentdir() .. "/" .. name .. "/proteins.fasta"
 
   values.nof_genes = stat_visitor.stats.nof_genes
   values.nof_coding_genes = stat_visitor.stats.nof_coding_genes

example-data/references/LbrM.1/ggline.gg

@@ -1 +1 @@
-LbrM.1: LbrM.01.0350:mRNA LbrM.01.0440:mRNA LbrM.01.0230:mRNA LbrM.01.0370:mRNA LbrM.01.0090:mRNA LbrM.01.0670:mRNA LbrM.01.0700:mRNA LbrM.01.0270:mRNA LbrM.01.0310:mRNA LbrM.01.0060:mRNA LbrM.01.0590:mRNA LbrM.01.0540:mRNA LbrM.01.0390:mRNA LbrM.01.0650:mRNA LbrM.01.0100:mRNA LbrM.01.0280:mRNA LbrM.01.0260:mRNA LbrM.01.0420:mRNA LbrM.01.0080:mRNA LbrM.01.0460:mRNA LbrM.01.0640:mRNA LbrM.01.0120:mRNA LbrM.01.0510:mRNA LbrM.01.0170:mRNA LbrM.01.0360:mRNA LbrM.01.0030:mRNA LbrM.01.0040:mRNA LbrM.01.0550:mRNA LbrM.01.0070:mRNA LbrM.01.0580:mRNA LbrM.01.0290:mRNA LbrM.01.0200:mRNA LbrM.01.0240:mRNA LbrM.01.0730:mRNA LbrM.01.0160:mRNA LbrM.01.0150:mRNA LbrM.01.0320:mRNA LbrM.01.0130:mRNA LbrM.01.0710:mRNA LbrM.01.0180:mRNA LbrM.01.0520:mRNA LbrM.01.0450:mRNA LbrM.01.0300:mRNA LbrM.01.0410:mRNA LbrM.01.0050:mRNA LbrM.01.0250:mRNA LbrM.01.0010:mRNA LbrM.01.0500:mRNA LbrM.01.0470:mRNA LbrM.01.0140:mRNA LbrM.01.0220:mRNA LbrM.01.0380:mRNA LbrM.01.0190:mRNA LbrM.01.0660:mRNA LbrM.01.0750:mRNA LbrM.01.0490:mRNA LbrM.01.0690:mRNA LbrM.01.0340:mRNA LbrM.01.0740:mRNA LbrM.01.0680:mRNA LbrM.01.0560:mRNA LbrM.01.0210:mRNA LbrM.01.0630:mRNA LbrM.01.0330:mRNA LbrM.01.0620:mRNA LbrM.01.0400:mRNA LbrM.01.0020:mRNA LbrM.01.0610:mRNA LbrM.01.0600:mRNA LbrM.01.0480:mRNA LbrM.01.0430:mRNA LbrM.01.0110:mRNA LbrM.01.0570:mRNA 
+LbrM.1: LbrM.01.0350:mRNA LbrM.01.0440:mRNA LbrM.01.0230:mRNA LbrM.01.0370:mRNA LbrM.01.0090:mRNA LbrM.01.0670:mRNA LbrM.01.0700:mRNA LbrM.01.0270:mRNA LbrM.01.0310:mRNA LbrM.01.0060:mRNA LbrM.01.0590:mRNA LbrM.01.0540:mRNA LbrM.01.0390:mRNA LbrM.01.0650:mRNA LbrM.01.0100:mRNA LbrM.01.0280:mRNA LbrM.01.0260:mRNA LbrM.01.0420:mRNA LbrM.01.0080:mRNA LbrM.01.0460:mRNA LbrM.01.0640:mRNA LbrM.01.0120:mRNA LbrM.01.0510:mRNA LbrM.01.0170:mRNA LbrM.01.0360:mRNA LbrM.01.0030:mRNA LbrM.01.0040:mRNA LbrM.01.0550:mRNA LbrM.01.0070:mRNA LbrM.01.0580:mRNA LbrM.01.0290:mRNA LbrM.01.0200:mRNA LbrM.01.0240:mRNA LbrM.01.0730:mRNA LbrM.01.0160:mRNA LbrM.01.0150:mRNA LbrM.01.0320:mRNA LbrM.01.0130:mRNA LbrM.01.0710:mRNA LbrM.01.0760:mRNA LbrM.01.0180:mRNA LbrM.01.0520:mRNA LbrM.01.0450:mRNA LbrM.01.0300:mRNA LbrM.01.0410:mRNA LbrM.01.0050:mRNA LbrM.01.0250:mRNA LbrM.01.0010:mRNA LbrM.01.0500:mRNA LbrM.01.0470:mRNA LbrM.01.0140:mRNA LbrM.01.0220:mRNA LbrM.01.0380:mRNA LbrM.01.0190:mRNA LbrM.01.0660:mRNA LbrM.01.0750:mRNA LbrM.01.0490:mRNA LbrM.01.0690:mRNA LbrM.01.0340:mRNA LbrM.01.0780:pseudogenic_transcript LbrM.01.0620:mRNA LbrM.01.0740:mRNA LbrM.01.0680:mRNA LbrM.01.0560:mRNA LbrM.01.0210:mRNA LbrM.01.0630:mRNA LbrM.01.0330:mRNA LbrM.01.0770:mRNA LbrM.01.0400:mRNA LbrM.01.0020:mRNA LbrM.01.0610:mRNA LbrM.01.0600:mRNA LbrM.01.0480:mRNA LbrM.01.0430:mRNA LbrM.01.0110:mRNA LbrM.01.0570:mRNA 

example-data/references/LbrM.1/metadata.json

@@ -1,14 +1,9 @@
 {
-  "pep":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/proteins.fasta",
-  "gff":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/annotation.gff3",
-  "gaf":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/go.gaf",
-  "genome":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/genome.fasta",
-  "nof_chromosomes":1,
-  "augustus_model":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/species/augustus_species",
+  "augustus_model":true,
   "name":"Leishmania braziliensis chromosome 1",
-  "nof_regions":1,
+  "nof_chromosomes":1,
   "nof_coding_genes":76,
   "nof_genes":76,
-  "chromosomes":"/Users/satta/uni/annot-nf/example-data/references/LbrM.1/chromosomes.fasta",
+  "nof_regions":1,
   "chromosome_pattern":"LbrM.([0-9.]+)$"
 }

example-data/references/LbrM.1/profile/default.qij

@@ -0,0 +1 @@
+blosum62.qij

example-data/references/LbrM.1/proteins.fasta

@@ -364,6 +364,14 @@ TSPDAISNDSGDPVDVLWSDVSFFLTEKRTQAVGLREGDAWRLRILAPRDTSRPEPPVDI
 LRLTPTIELLRIPGDSAVEEYVLFDANSNSLACTDLYHGEYADLDPANSWMCRVWFMKRG
 DYKHKGLVPRYKWLQILQQGSLSVIQSAIDELTRRRPIKCVLSAHGTPPLNGDDAVNTLR
 RQWSLPPLHPTERPRDGRK*
+>LbrM.01.0760:mRNA
+MPRATPIALPAARWCLAFASSAPTASSLPLTSSAATPVESYQDNRPRLAPRALRSGIKAI
+NSRRLGAAPHSLPSLCRRPSNLWVRCCSGNAGCRAVSSAPSLPASAGTAAKSTSAAHPTP
+PAPAPALQERRVCPECGKHFLRESNLVHHRTTRHGVQVASASKVARAELAMRNAQLQQEL
+ARAQARVKQLREGSDSAARQERDSAATEPTDDATTRAYPSAVMTGRLMEVDEAVERAWRH
+SGRGLGTGVSFVVCIGTVLGPVEVGTLRGATPSSAADSSATGPRVLQFKLEVHGYRERRP
+GQLKMYRAHLLVRYVAWQPYHRYGDGDGAGSGAAASSPSSTAPLPFKVQEGDLLRVQGHY
+ALHTSHDMVSKQSAENVVLEADAVGLLRPAPAKEAPAVPAGGGGEGDGSPTRQRQ*
 >LbrM.01.0180:mRNA
 MALPGVSHYERIPTRTKIQFFWISMLTMGFAYQFLKMTVLRVQPKREEQMYLHIQKVYGD
 NVPEELLRRAKRQREAQDALALTNMLRTPTPGQTSNALQNELDPRALISLRSWNGH*
@@ -516,6 +524,35 @@ TAPIILDTVNFEPAQKKVTPEDIAAYEWLRVKESVEGTDAATLFAKLSKWKDDVLGLSVP
 EILRRDYKQFNFKARTKKGVMSTGTSSVPCTCKQLEGHFSVNMVVEEAAKYMEQHQLDVL
 VFTFSGQASGKHSREIAFCAKPDTMSVFASFVTEAPSGLSFTKITKCPTADGSYEYTSYS
 LSDPSISRKKLVPVLSEFLAEGTRSLL*
+>LbrM.01.0780:pseudogenic_transcript
+MSGASPATPTPNDAPPPITIAAASFTAEDLNASTTAIPVAKGSAHLNAKLLMVNLGQDVQ
+ATVLNRFRNLQGTIHSQLRNLQNNVANLHHSTPASRLSHCRTAGSTTTTNSALAIHSLRK
+LFDVIEQRYSHVSILLLLCNVGFEAAAFGIYLHVQSNHITENWREFDWGLRYFIAEVLLS
+AVFMASWISLLAVEAKKWAYVLTARSLMNYLSSGWMLLLALGALLTLDRAWTRVYAPMFL
+RVWWLHESLLSLLHYPQISAHFTENRLEMVRSMIQCIAVIGISVGILQAVESFCGDPVEY
+FEMVYMMLLSFSSIGYGDVTPLTVQGRLLMIVFIGVGFSYFVPILQYVADLGVYHLSHAY
+YTTWLKRTDHVVICGNLGYNELRMQLKNIFAEDRHYLKMKVVLLLREQPSAQVLLLLNSP
+KYRSAVHLLVGDPGVPTDIDRCNARGASAMFLLGAGTNSSYYSDYDLAAQAMTVSALVPD
+LPLYILLHRSRYTKSLMPSRANVLEFERLNHNLLGLGCVLPGMIPFVANLMRMFDPMTTE
+ALWELRDLKDLFGFRGSKASLRAMRKMWTPKRAMLTYGAATIELGNGAEPDWMSTYEASL
+AQHVDTVAAPTPVQRGHYTVVSLARLLYSTDITLIGVVRDSGSGDSIVDLAPRGSLVGVQ
+KLIVICDVRRAAQGVVDEIVHDALLHPTQRGSPTSAKMPQHELLHNPKQHPHRRSDSASS
+AAATAATVLGAGAVERPRRQPRVEAKRDAEGRMPLAAVSPVPSAAADDEDALIEALVSPV
+LLDAGRLGSLACESASAGAPVTVTQSSPVFPVPTAAHSVLRVESDVRHLANHYVFIDLSS
+AHERTNWSPEAAVESRTAKAADYYDTMRPVRQHNPDSDIVLLASDTNYDSLNNMWEEEDV
+TGSLIVVQGCGLFTSDLRRCNVAKAAAIVIFSAGDRCDDHGDSLSVLVMQLVRQLIDEDK
+HNGAADIPIVVEVDHAELVPLFGPATTVGKDAKTSEWVLEPSFMSGCVVCRHMLDTGLQE
+MHFTPELLHVLEQLLSSKSESLLVTVMAPDAAWVVYEDATSFGLDNALLPLAIHRFHEIL
+RDNNSIPFRYIITNPPPSFPLHSDDFIYCLKL*
+>LbrM.01.0620:mRNA
+MPLPQNQDDFSAYTEIDLPTETRIDAIRRTALANQEWVACEKVHGTNFAIYLLNESEVRF
+AKRSGIMDPNENFFGYHLLIDDFTAQVRALCELLKRKYGVTGRMGRVVLHGELFGAKYTH
+PLVPKSAKWCVLPNKKRVPISGVEIQSEAFPQYSPELHYFAFDIKYSVSGAEEAMVLLPF
+DDFTEVCSQVPHLLYAKPLVRGTLDECLAFDVENFITPLPALLGLGNYPLEGNLAEGVVI
+RHVRRGDPAVECSGVSTIIKLRCSSFMELKHPGKQQELKATFLDTVRAGALQRMRGGKKV
+TVLTDAMLPKLEAAANALLLNNVSKGRLNNVLSKIGREPLLSGEVQEEDVVLMLAQDALK
+DFLKETDPVVLNTSLSFRKALIRSVYFAAEDLLRGEWKRIMERERASQTEIDAAIAALEK
+EEAQ*
 >LbrM.01.0740:mRNA
 MSQQDRVAPQDQDSFLDDQPGVRPIPSFDDMPLHQNLLRGIYSYGFEKPSSIQQRAIAPF
 TRGGDIIAQAQSGTGKTGAFSIGLLQRLDFRHNLIQGLVLSPTRELALQTAEVISRIGEF
@@ -594,15 +631,24 @@ SVSGAPQQPPSLSCPWPVHPIVQKASCAPHVVLLTSGNADEHELPLAHQLGVKLNACGVH
 NVSILRGGVASLRRALPELVVRRVPSL*
 >LbrM.01.0330:mRNA
 MTRGNQRDLAREKNMKKQQEKSKGHRDNGLSYASRKEADAERMRQKQAAADERKNAGGS*
->LbrM.01.0620:mRNA
-MPLPQNQDDFSAYTEIDLPTETRIDAIRRTALANQEWVACEKVHGTNFAIYLLNESEVRF
-AKRSGIMDPNENFFGYHLLIDDFTAQVRALCELLKRKYGVTGRMGRVVLHGELFGAKYTH
-PLVPKSAKWCVLPNKKRVPISGVEIQSEAFPQYSPELHYFAFDIKYSVSGAEEAMVLLPF
-DDFTEVCSQVPHLLYAKPLVRGTLDECLAFDVENFITPLPALLGLGNYPLEGNLAEGVVI
-RHVRRGDPAVECSGVSTIIKLRCSSFMELKHPGKQQELKATFLDTVRAGALQRMRGGKKV
-TVLTDAMLPKLEAAANALLLNNVSKGRLNNVLSKIGREPLLSGEVQEEDVVLMLAQDALK
-DFLKETDPVVLNTSLSFRKALIRSVYFAAEDLLRGEWKRIMERERASQTEIDAAIAALEK
-EEAQ*
+>LbrM.01.0770:mRNA
+MDKRRSSWREWFRLGRRSDRPQVFADKHYAHSEHPFLSLRKFVEFLDRRHTNVSIFGLLM
+HITMEIVSIAFYVWTSHVTAATSATEFTWSVPVFITEVALSIIFLLAWIGLFFLEHDKKA
+YLISWLSLVNAMTSIPMIVIGIGALKDSLWRSVWVPMFLRVWWLCDSLNVLIDYPQIARR
+TPEVWREMMRYFLRLLAVMGTCIGTHQIVESCSGQYIDLYDSLYLIIVAFATIGFGDVTS
+TTTPARVFMVAFIVIGICFFLPLFQRLALIAERRQFHNTFSGGSASWFRRGWKHPHVIIC
+GQFSDLSVELLLRNFYAGWRKYLDTCIVLMAPEEHSPEVRLVANLPWLKSRVTLMVGNPE
+NSKDLDRAKARDADAIFLFGDSRSAAYYQDYTIVAQSVAVSLYDRNLPQHLLLHRNCTVK
+QISPYAASVLEVERTLHHLLGLSMTHPGVVPLIINLLRTYESLPSDITLSRDWVEQYEYS
+LRNDMYGLEIPDALRGREFRVLARAFFEKDVTLIGILNVRSVVQLNPRELVPNARKLILI
+AKTMKVAQDATDAIARDYEQTFGEEMLVAPDPDEHDRAKRRLVRSRYHTEFSSNDSTLDD
+NVGSVNGTAKQRGPPMRPHGAEAVLETPDPLGRLSHVPVSLQTTGSSIAAEGDFDDEFDA
+RNSSVGAAPSLPSSVHPSEVRSEALVRIDDAFDLENHFVIIDLSTAKAKDESSRYAQEAV
+STAVAHDIFHVTVPLRQAHPASDIVLLTNDVSFGPYFDYYWSVHHQDSAYPVKYICGCGL
+NTADLRRCNLERCAGCCVFYAGDISLSGSTSAMSMLTVLSINDILHGIPAFPVVVELEGL
+VNLPLFPPHAEDPRLRSKAEIDFVYEPNFIIGNAVSRLMLFPALQRTYFMEEFIDVMDVL
+ISGHAPDTPALARLPLSLCEADLHTYEDVVIYCLKFGFLPIALQRRIVDMCNPSINGQRF
+VLTNPPRALPVRQQTDLVFYITPG*
 >LbrM.01.0400:mRNA
 MCSLETLLCSPADLIAECPVIGPSDVRLVAANFEAILNKCLYCVRLKLPTPLRVLLTIIG
 DAGELQANKVCLALLQPTEEGTCVDVFCDLAAQLLGRRAAVLRLQFDVEVLFQVMQLFCC

example-data/references/LmjF.1/ggline.gg

@@ -1 +1 @@
-LmjF.1: LmjF.01.0090:mRNA LmjF.01.0450:mRNA LmjF.01.0730:mRNA LmjF.01.0120:mRNA LmjF.01.0315:mRNA LmjF.01.0680:mRNA LmjF.01.0660:mRNA LmjF.01.0710:mRNA LmjF.01.0600:mRNA LmjF.01.0320:mRNA LmjF.01.0440:mRNA LmjF.01.0760:mRNA LmjF.01.0520:mRNA LmjF.01.0140:mRNA LmjF.01.0280:mRNA LmjF.01.0470:mRNA LmjF.01.0300:mRNA LmjF.01.0410:mRNA LmjF.01.0540:mRNA LmjF.01.0130:mRNA LmjF.01.0740:mRNA LmjF.01.0260:mRNA LmjF.01.0330:mRNA LmjF.01.0550:mRNA LmjF.01.0250:mRNA LmjF.01.0310:mRNA LmjF.01.0010:mRNA LmjF.01.0020:mRNA LmjF.01.0390:mRNA LmjF.01.0210:mRNA LmjF.01.0100:mRNA LmjF.01.0400:mRNA LmjF.01.0430:mRNA LmjF.01.0335:mRNA LmjF.01.0150:mRNA LmjF.01.0030:mRNA LmjF.01.0360:mRNA LmjF.01.0490:mRNA LmjF.01.0160:mRNA LmjF.01.0040:mRNA LmjF.01.0060:mRNA LmjF.01.0350:mRNA LmjF.01.0460:mRNA LmjF.01.0080:mRNA LmjF.01.0190:mRNA LmjF.01.0790:mRNA LmjF.01.0780:mRNA LmjF.01.0770:mRNA LmjF.01.0750:mRNA LmjF.01.0270:mRNA LmjF.01.0720:mRNA LmjF.01.0700:mRNA LmjF.01.0380:mRNA LmjF.01.0500:mRNA LmjF.01.0690:mRNA LmjF.01.0290:mRNA LmjF.01.0670:mRNA LmjF.01.0650:mRNA LmjF.01.0610:mRNA LmjF.01.0110:mRNA LmjF.01.0630:mRNA LmjF.01.0240:mRNA LmjF.01.0620:mRNA LmjF.01.0640:mRNA LmjF.01.0800:mRNA LmjF.01.0570:mRNA LmjF.01.0050:mRNA LmjF.01.0590:mRNA LmjF.01.0230:mRNA LmjF.01.0560:mRNA LmjF.01.0530:mRNA LmjF.01.0370:mRNA LmjF.01.0170:mRNA LmjF.01.0180:mRNA LmjF.01.0510:mRNA LmjF.01.0480:mRNA LmjF.01.0420:mRNA LmjF.01.0070:mRNA LmjF.01.0580:mRNA LmjF.01.0220:mRNA LmjF.01.0340:mRNA LmjF.01.0200:mRNA 
+LmjF.1: LmjF.01.0090:mRNA LmjF.01.0450:mRNA LmjF.01.0730:mRNA LmjF.01.0120:mRNA LmjF.01.0315:mRNA LmjF.01.0680:mRNA LmjF.01.0660:mRNA LmjF.01.0710:mRNA LmjF.01.0600:mRNA LmjF.01.0320:mRNA LmjF.01.0440:mRNA LmjF.01.0760:mRNA LmjF.01.0520:mRNA LmjF.01.0140:mRNA LmjF.01.0280:mRNA LmjF.01.0470:mRNA LmjF.01.0300:mRNA LmjF.01.0410:mRNA LmjF.01.0540:mRNA LmjF.01.0130:mRNA LmjF.01.0740:mRNA LmjF.01.0260:mRNA LmjF.01.0330:mRNA LmjF.01.0550:mRNA LmjF.01.0250:mRNA LmjF.01.0310:mRNA LmjF.01.0010:mRNA LmjF.01.0020:mRNA LmjF.01.0390:mRNA LmjF.01.0210:mRNA LmjF.01.0100:mRNA LmjF.01.0400:mRNA LmjF.01.0430:mRNA LmjF.01.0335:mRNA LmjF.01.0150:mRNA LmjF.01.0030:mRNA LmjF.01.0360:mRNA LmjF.01.0490:mRNA LmjF.01.0160:mRNA LmjF.01.0040:mRNA LmjF.01.0830:mRNA LmjF.01.0060:mRNA LmjF.01.0230:mRNA LmjF.01.0810:mRNA LmjF.01.0350:mRNA LmjF.01.0460:mRNA LmjF.01.0080:mRNA LmjF.01.0190:mRNA LmjF.01.0790:mRNA LmjF.01.0780:mRNA LmjF.01.0770:mRNA LmjF.01.0750:mRNA LmjF.01.0270:mRNA LmjF.01.0720:mRNA LmjF.01.0700:mRNA LmjF.01.0380:mRNA LmjF.01.0500:mRNA LmjF.01.0690:mRNA LmjF.01.0290:mRNA LmjF.01.0670:mRNA LmjF.01.0650:mRNA LmjF.01.0610:mRNA LmjF.01.0110:mRNA LmjF.01.0630:mRNA LmjF.01.0240:mRNA LmjF.01.0620:mRNA LmjF.01.0640:mRNA LmjF.01.0800:mRNA LmjF.01.0570:mRNA LmjF.01.0050:mRNA LmjF.01.0590:mRNA LmjF.01.0820:mRNA LmjF.01.0560:mRNA LmjF.01.0530:mRNA LmjF.01.0370:mRNA LmjF.01.0170:mRNA LmjF.01.0180:mRNA LmjF.01.0510:mRNA LmjF.01.0480:mRNA LmjF.01.0420:mRNA LmjF.01.0070:mRNA LmjF.01.0580:mRNA LmjF.01.0220:mRNA LmjF.01.0340:mRNA LmjF.01.0200:mRNA 

example-data/references/LmjF.1/metadata.json

@@ -1,15 +1,10 @@
 {
-  "pep":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/proteins.fasta",
-  "gff":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/annotation.gff3",
-  "gaf":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/go.gaf",
-  "genome":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/genome.fasta",
   "nof_chromosomes":1,
-  "nof_regions":1,
-  "augustus_model":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/species/augustus_species",
+  "chromosome_pattern":"LmjF.(%d+)",
   "name":"Leishmania major Friedlin chromosome 1",
-  "snap_model":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/snap.hmm",
+  "snap_model":true,
   "nof_coding_genes":85,
-  "nof_genes":85,
-  "chromosomes":"/Users/satta/uni/annot-nf/example-data/references/LmjF.1/chromosomes.fasta",
-  "chromosome_pattern":"LmjF.(%d+)"
+  "augustus_model":true,
+  "nof_regions":1,
+  "nof_genes":85
 }

example-data/references/LmjF.1/profile/default.qij

@@ -0,0 +1 @@
+blosum62.qij