diff --git a/README.md b/README.md
index 4230fc81c15248ed82b4065cde87f0b45238442c..a77e16d501c3b57eb4c0dd4adc29d650598a5fa3 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,29 @@ Here are the requirements and the used versions.
User should edit these commands to fit the current RVDB version:
```sh
-wget https://hive.biochemistry.gwu.edu/prd/rvdb/content/U-RVDBv15.1.fasta
+RVDB_VERSION=19.0
+mkdir -p ${RVDB_VERSION} && cd ${RVDB_VERSION}
+
+# a place where temporary files will be written
+RVDB_SCRATCH_DIR=$myscratchdir/rvdb${RVDB_VERSION}
+# taxadb can be generated or downloaded (please refer to taxadb website)
+taxadb=/my/databases/taxadb_full.sqlite
+# the directory containing this readme file and the rvdb-prot scripts
+rvdbPipeline=$HOME/my/bioinformatics/rvdb-prot/
+
+
+RVDB_ORIG_DIR=${PWD}
+wget https://rvdb.dbi.udel.edu/download/U-RVDBv${RVDB_VERSION}.fasta.gz
+mkdir -p ${RVDB_SCRATCH_DIR}
+
+# here is an example running snakemake with a slurm cluster manager, adapt it to your needs
+
+slurmpartition="common"
+slurmqos="normal"
+
+# this variable is needed for snakemake to launch subsequent jobs
export sbcmd="sbatch --cpus-per-task={threads} --mem={cluster.mem} --partition={cluster.partition} --qos={cluster.qos} --out={cluster.out} --error={cluster.error} --job-name={cluster.name} {cluster.extra}"
-snakemake --rerun-incomplete --snakefile ~/dev/rvdb/pipeline/Snakefile -p -pr --local-cores 1 --jobs 1000 --cluster-config slurm.json --cluster \"$sbcmd\" --config origNucl=U-RVDBv15.1.fasta
+
+
+sbatch --qos ${slurmqos} --partition ${slurmpartition} -c 1 --job-name=rvdb${RVDB_VERSION} --wrap="snakemake --rerun-incomplete --snakefile $rvdbPipeline/pipeline/Snakefile -p -pr --local-cores 1 --jobs 1000 --cluster-config $rvdbPipeline/slurm.json --cluster \"$sbcmd\" --config origNucl=${RVDB_ORIG_DIR}/U-RVDBv${RVDB_VERSION}.fasta.gz scratchDir=${RVDB_SCRATCH_DIR} sampleName=rvdb${RVDB_VERSION} taxadb=$taxadb prefix=U-RVDBv${RVDB_VERSION}"
```
diff --git a/annotate/annotations_schema.sql b/annotate/annotations_schema.sql
index ae46593440ecffc49048570d5799cf9a69d2a3c6..16a3fc868cfd22316533b599e49e32cf2dddf331 100644
--- a/annotate/annotations_schema.sql
+++ b/annotate/annotations_schema.sql
@@ -10,7 +10,7 @@ CREATE TABLE keyword(
str CHAR(30) UNIQUE
);
-CREATE TABLE fam_kw_unsorted(
+CREATE TABLE fam_kw_seqnames_unsorted(
famId INTEGER,
kwId INTEGER,
freq INTEGER,
@@ -19,7 +19,25 @@ CREATE TABLE fam_kw_unsorted(
PRIMARY KEY(famId,kwId)
);
-CREATE TABLE fam_kw(
+CREATE TABLE fam_kw_ref_unsorted(
+ famId INTEGER,
+ kwId INTEGER,
+ freq INTEGER,
+ FOREIGN KEY(famId) REFERENCES family(id),
+ FOREIGN KEY(kwId) REFERENCES keyword(id),
+ PRIMARY KEY(famId,kwId)
+);
+
+CREATE TABLE fam_kw_seqnames(
+ famId INTEGER,
+ kwId INTEGER,
+ freq INTEGER,
+ FOREIGN KEY(famId) REFERENCES family(id),
+ FOREIGN KEY(kwId) REFERENCES keyword(id),
+ PRIMARY KEY(famId,kwId)
+);
+
+CREATE TABLE fam_kw_ref(
famId INTEGER,
kwId INTEGER,
freq INTEGER,
diff --git a/annotate/makeAnnotationsIntoSQL.py b/annotate/makeAnnotationsIntoSQL.py
index bb45d6dc3de939883c9d960fa2a3967ea6be9384..a240f3b702d4efd8ee7d452a1ce3ddc7b1941eb1 100644
--- a/annotate/makeAnnotationsIntoSQL.py
+++ b/annotate/makeAnnotationsIntoSQL.py
@@ -18,32 +18,37 @@ def getClusterInfo(HMMpath):
if line.startswith("//"):
clusterInfo = {"id": currID, "length": currLength}
if line.split() == ("HMM"):
- print("plop")
break
return clusterInfo
def extractSeqNames(MSApath):
currMSA = open(MSApath)
- annotations = []
+ seqNameAnnotations = []
for line in currMSA:
if line.startswith(">"):
- annotations.append(line)
+ seqNameAnnotations.append(line)
currMSA.close()
- return annotations
+ return seqNameAnnotations
-def wordCount(annotList):
+def extractHMMannots(tbloutPath):
+ lines = (" ".join(l.split()[18:]) for l in open(tbloutPath) if not l.startswith("#"))
+ return list(lines)
+
+
+def wordCount(annotList,directName):
wc = defaultdict(int)
for currAnnot in annotList:
- words = re.findall(r"\w{3,}",currAnnot.split("|")[5])
+ field = currAnnot if directName else currAnnot.split("|")[5]
+ words = re.findall(r"\w{3,}",field)
for word in words:
- wc[word] += 1
+ wc[word.lower()] += 1
return wc
-def getTaxInfo(tdb_accession,tdb_taxid,annotations):
- taxInfo = {"nbSeq":len(annotations)}
+def getTaxInfo(tdb_accession,tdb_taxid,seqNameAnnotations):
+ taxInfo = {"nbSeq":len(seqNameAnnotations)}
accs = []
- for ca in annotations:
+ for ca in seqNameAnnotations:
#accs.append(re.findall("[A-Z0-9\._]{5,10}",ca)[0].split(".")[0])
accs.append(ca.split("|")[2].split(".")[0])
taxInfo["taxid"] = []
@@ -82,7 +87,7 @@ def getTaxInfo(tdb_accession,tdb_taxid,annotations):
return taxInfo
-def writeAnnotations(dbConn,famID,clusterInfo,taxInfo,annotations):
+def writeAnnotations(dbConn,famID,clusterInfo,taxInfo,seqNameAnnotations,refHMMannotations):
c = dbConn.cursor()
c.execute("INSERT INTO family VALUES ({id},{size},{nbSeq},{LCAtaxid});".format(
id=famID,
@@ -92,18 +97,19 @@ def writeAnnotations(dbConn,famID,clusterInfo,taxInfo,annotations):
))
c.executemany("INSERT INTO fam_tax VALUES ({},?,?);".format(famID),taxInfo["taxon"].items())
- wc = wordCount(annotations)
- for currWord,currCount in wc.items():
- c.execute("SELECT id FROM keyword WHERE str = ? ;",(currWord,))
- data=c.fetchone()
- if data is None:
- c.execute("INSERT INTO keyword (str) VALUES (?) ;",(currWord,))
- cwid = c.lastrowid
- else:
- cwid = data[0]
- c.execute("INSERT INTO fam_kw_unsorted VALUES (?,?,?);",(famID,cwid,currCount))
+ for (annotations,table,directName) in ((seqNameAnnotations,"fam_kw_seqnames_unsorted",False),(refHMMannotations,"fam_kw_ref_unsorted",True)):
+ wc = wordCount(annotations,directName)
+ for currWord,currCount in wc.items():
+ c.execute("SELECT id FROM keyword WHERE str = ? ;",(currWord,))
+ data=c.fetchone()
+ if data is None:
+ c.execute("INSERT INTO keyword (str) VALUES (?) ;",(currWord,))
+ cwid = c.lastrowid
+ else:
+ cwid = data[0]
+ c.execute(f"INSERT INTO {table} VALUES (?,?,?);",(famID,cwid,currCount))
- dbConn.commit()
+ dbConn.commit()
@@ -111,6 +117,7 @@ def writeAnnotations(dbConn,famID,clusterInfo,taxInfo,annotations):
parser = argparse.ArgumentParser()
parser.add_argument("hmmDir", help="hmm dir")
parser.add_argument("alignedDir", help="directory containing .msa.faa")
+parser.add_argument("annotResultsDir", help="directory containing tblout resulting a reference DB query to annotate")
parser.add_argument("taxadb", help="taxadb file")
parser.add_argument("schema", help="sql schema to format the db")
parser.add_argument("annotDB", help="db to create in which annotation will be stored")
@@ -128,18 +135,24 @@ tdb_taxid = TaxID(dbtype='sqlite', dbname=args.taxadb)
clusterList = glob.glob(args.hmmDir+"/*.hmm")
for currCluster in clusterList:
familyName = os.path.basename(currCluster)[:-4]
- clusterInfo = getClusterInfo("%s/%s.hmm"%(args.hmmDir,familyName))
+ clusterInfo = getClusterInfo(f"{args.hmmDir}/{familyName}.hmm")
if not clusterInfo:
- print("Failed to read {}".format(familyName))
+ print(f"Failed to read {familyName}")
continue
- annotations = extractSeqNames("%s/%s.fasta"%(args.alignedDir,familyName))
- taxInfo = getTaxInfo(tdb_accession,tdb_taxid,annotations)
- writeAnnotations(conn,clusterInfo["id"],clusterInfo,taxInfo,annotations)
+ seqNameAnnotations = extractSeqNames(f"{args.alignedDir}/{familyName}.fasta")
+ refHMMannotations = extractHMMannots(f"{args.annotResultsDir}/{familyName}.tblout")
+ taxInfo = getTaxInfo(tdb_accession,tdb_taxid,seqNameAnnotations)
+ writeAnnotations(conn,clusterInfo["id"],clusterInfo,taxInfo,seqNameAnnotations,refHMMannotations)
# now we need to sort the table fam_kw_unsorted
c = conn.cursor()
-c.execute("INSERT INTO fam_kw SELECT * FROM fam_kw_unsorted ORDER BY freq DESC;")
-c.execute("DROP TABLE fam_kw_unsorted;")
+c.execute("INSERT INTO fam_kw_seqnames SELECT * FROM fam_kw_seqnames_unsorted ORDER BY freq DESC;")
+c.execute("DROP TABLE fam_kw_seqnames_unsorted;")
+conn.commit()
+
+c = conn.cursor()
+c.execute("INSERT INTO fam_kw_ref SELECT * FROM fam_kw_ref_unsorted ORDER BY freq DESC;")
+c.execute("DROP TABLE fam_kw_ref_unsorted;")
conn.commit()
conn.close()
diff --git a/annotate/sqlAnnotToTxt.py b/annotate/sqlAnnotToTxt.py
index 59d4e5ad7d477ba68305bea453b142b884babf5d..f7cb72af3c97dc15afa728fadc4d2b78c44efced 100644
--- a/annotate/sqlAnnotToTxt.py
+++ b/annotate/sqlAnnotToTxt.py
@@ -28,7 +28,16 @@ for currFamR in ccf.execute('SELECT * FROM family'):
o = open("{dir}/{prefix}{id}.txt".format(dir=args.txtDir,prefix=args.prefix,id=currF),"w")
lineage = tdb_taxid.lineage_name(int(currLCA), reverse=True)
o.write("LENGTH\t{length}\nLCA\t{lca}\nNBSEQ\t{nbseq}\nKEYWORDS:\n".format(length=currSize,lca=("::".join(tdb_taxid.lineage_name(int(currLCA), reverse=True)) if lineage else ""),nbseq=currNbseq))
- for currFreq,currKw in ckw.execute('select freq,str from fam_kw JOIN keyword ON fam_kw.kwId = keyword.id WHERE fam_kw.famID=? order by freq desc',(currF,)):
+
+ # keywords from reference database
+ kw_string = []
+ for currFreq,currKw in ckw.execute('select freq,str from fam_kw_ref JOIN keyword ON fam_kw_ref.kwId = keyword.id WHERE fam_kw_ref.famID=? order by freq desc',(currF,)):
+ kw_string.append((f"{currKw}\t{currFreq}"))
+ o.write( "\n".join(kw_string) if kw_string else "--" )
+
+ # keywords from sequence names
+ o.write("\nKEYWORDS FROM SEQUENCES:\n")
+ for currFreq,currKw in ckw.execute('select freq,str from fam_kw_seqnames JOIN keyword ON fam_kw_seqnames.kwId = keyword.id WHERE fam_kw_seqnames.famID=? order by freq desc',(currF,)):
o.write("{kw}\t{count}\n".format(kw=currKw.strip("[]()"),count=currFreq))
o.write("SEQUENCES:\n")
with open("aligned/FAM{famName}.fasta".format(famName = str(currF).zfill(6))) as f:
diff --git a/pipeline/Snakefile b/pipeline/Snakefile
index 6fac37038a4af4aee96fab72c8aac12f8476cb0f..94c6c67eb85f593a4dcd5f20fcb53f02523946e9 100644
--- a/pipeline/Snakefile
+++ b/pipeline/Snakefile
@@ -1,11 +1,12 @@
-localrules: ConvProt_splitInNames, ConvProt_mergeFasta, Profiles_splitProtFasta, Profiles_makeBlastDB, Profiles_blastToClusters, Profiles_clustersToFamilies, Pofiles_mergeBlast, Profiles_genAnnot, Profiles_mergeHmm, origNucl,Profiles_genTxtAnnot
+localrules: ConvProt_splitInNames, ConvProt_mergeFasta, Profiles_splitProtFasta, Profiles_makeBlastDB, Profiles_blastToClusters, Profiles_clustersToFamilies, Pofiles_mergeBlast, Profiles_genAnnot, Profiles_mergeHmm, origNucl,Profiles_genTxtAnnot, bz2Results, zipResults
-workdir: "/pasteur/scratch/users/tbigot/rvdb"
-jobname="rvdb"
+origDir = os.getcwd()
+prefix = config["prefix"]
-shell("mkdir -p logs/cluster")
+workdir: config["scratchDir"]
+sampleName = config["sampleName"]
-sampleName = "rvdb"
+shell("mkdir -p logs/cluster")
def annot_input(wildcards):
txtAnnot_dir = checkpoints.Profiles_genTxtAnnot.get(**wildcards).output[0]
@@ -15,21 +16,38 @@ def annot_input(wildcards):
rule all:
input:
- "prot.hmm",
- "prot-hmm.sqlite",
+ f"{origDir}/{prefix}-prot.fasta.bz2",
+ f"{origDir}/{prefix}-prot.hmm.bz2",
+ f"{origDir}/{prefix}-prot-hmm.sqlite.bz2",
+ f"{origDir}/{prefix}-prot-hmm-txt.zip",
+
+rule bz2Results:
+ output:
+ f"{origDir}/{prefix}-{{f}}.bz2"
+ input:
+ "{f}"
+ shell:
+ "bzip2 -z -c {input} > {output}"
+
+rule zipResults:
+ output:
+ f"{origDir}/{prefix}-prot-hmm-txt.zip",
+ input:
annot_input
+ shell:
+ "zip -r {output} annot"
checkpoint Profiles_genTxtAnnot:
input:
sqlite = "prot-hmm.sqlite",
- taxadb = "/local/databases/rel/taxadb/current/db/taxadb_full.sqlite",
+ taxadb = config["taxadb"],
params:
txtDir = "annot/",
output:
directory("annot")
shell:
"mkdir {output}; "
- "module load Python/3.6.0 ; python3 {workflow.basedir}/../annotate/sqlAnnotToTxt.py {input.sqlite} {params.txtDir} {input.taxadb}"
+ "python3 {workflow.basedir}/../annotate/sqlAnnotToTxt.py {input.sqlite} {params.txtDir} {input.taxadb}"
checkpoint Profiles_clustersToFamilies:
input:
@@ -48,27 +66,36 @@ def input_all_Hmm(wildcards):
fam_dir = checkpoints.Profiles_clustersToFamilies.get(**wildcards).output[0]
return expand("hmm/{famId}.hmm",famId = glob_wildcards(os.path.join(fam_dir, "{i}.fasta")).i)
+def input_all_AgainstRef(wildcards):
+ fam_dir = checkpoints.Profiles_clustersToFamilies.get(**wildcards).output[0]
+ return expand("against_ref/{famId}.tblout",famId = glob_wildcards(os.path.join(fam_dir, "{i}.fasta")).i)
+
rule Profiles_genAnnot:
- input: input_all_Hmm
+ input:
+ allHmm = input_all_Hmm,
+ allAgainstRef = input_all_AgainstRef
output:
"prot-hmm.sqlite"
params:
hmmDir = "hmm",
alignedDir = "aligned",
- taxaDB = "/local/databases/rel/taxadb/current/db/taxadb_full.sqlite",
- schema = "{}/../annotate/annotations_schema.sql".format(workflow.basedir)
+ annotResults = "against_ref",
+ taxaDB = config["taxadb"],
+ schema = f"{workflow.basedir}/../annotate/annotations_schema.sql"
shell:
- "module load Python/3.6.0 ; python3 {workflow.basedir}/../annotate/makeAnnotationsIntoSQL.py {params.hmmDir} {params.alignedDir} {params.taxaDB} {params.schema} {output}"
+ "python3 {workflow.basedir}/../annotate/makeAnnotationsIntoSQL.py {params.hmmDir} {params.alignedDir} {params.annotResults} {params.taxaDB} {params.schema} {output}"
rule Profiles_mergeHmm:
input: input_all_Hmm
output:
"prot.hmm"
- run:
- for hmm in input:
- shell("cat {hmm} >> {output}")
+ shell:
+ """
+ find hmm -maxdepth 1 -type f -name '*.hmm' -print0 |
+ xargs -0 cat > {output}
+ """
rule Profiles_hmmbuild:
input:
@@ -77,7 +104,20 @@ rule Profiles_hmmbuild:
hmm="hmm/{part}.hmm",
log="hmm/{part}.log"
run:
- shell("module load hmmer/3.2.1 ; hmmbuild --informat afa -n {wildcards.part} -o {output.log} {output.hmm} {input}")
+ shell("hmmbuild --cpu {threads} --informat afa -n {wildcards.part} -o {output.log} {output.hmm} {input}")
+
+rule Profiles_family_against_ref:
+ input:
+ "families/{part}.fasta"
+ output:
+ tblout="against_ref/{part}.tblout",
+ log="against_ref/{part}.log"
+ params:
+ pfam="/local/databases/rel/pfam/current/hmmer/3.1/Pfam-A.hmm",
+ options="--cut_ga"
+ shell:
+ "hmmscan {params.options} --tblout {output.tblout} -o {output.log} {params.pfam} {input}"
+
rule Profiles_align:
input:
@@ -85,9 +125,9 @@ rule Profiles_align:
output:
"aligned/{part}.fasta"
threads:
- 1
+ 12
shell:
- "module load fasta mafft && mafft --thread {threads} --anysymbol --auto {input} > {output}"
+ "mafft --thread {threads} --anysymbol --auto {input} > {output}"
rule Profiles_blastToClusters:
@@ -99,19 +139,27 @@ rule Profiles_blastToClusters:
params:
prefix="FAM"
shell:
- "module load silix && silix {input.fasta} {input.blastall} -f {params.prefix} > {output}"
+ "silix {input.fasta} {input.blastall} -f {params.prefix} > {output}"
-rule Profiles_splitProtFasta:
+checkpoint Profiles_splitProtFasta:
input:
"prot_collapsed.fasta"
output:
- dynamic("prot.split/{part}.fasta")
+ directory("prot.split")
params:
chunkSize=1500,
suffix=".fasta",
shell:
- "python3 {workflow.basedir}/../build/splitFasta.py {input} prot.split/ --suffix {params.suffix} --maxChunkSize {params.chunkSize}"
-
+ """
+ mkdir {output}
+ python3 {workflow.basedir}/../build/splitFasta.py {input} prot.split/ --suffix {params.suffix} --maxChunkSize {params.chunkSize}
+ """
+
+def get_output_Profiles_splitProtFasta(w):
+ odir = checkpoints.Profiles_splitProtFasta.get(**w).output[0]
+ return glob_wildcards(os.path.join(odir, "{i}.fasta")).i
+
+
rule Profiles_collapse:
input:
"{part}.fasta"
@@ -120,15 +168,15 @@ rule Profiles_collapse:
params:
fractionCoverage = "",
fractionId = 1,
- memory = 4500
+ memory = 10000
threads:
12
shell:
- "module load blast/2.2.26 cd-hit/4.6.6 && cd-hit -i {input} -o {output} {params.fractionCoverage} -s {params.fractionId} -T {threads} -M {params.memory}"
+ "cd-hit -i {input} -o {output} {params.fractionCoverage} -s {params.fractionId} -T {threads} -M {params.memory}"
rule Pofiles_mergeBlast:
input:
- dynamic("blast.split/{part}.blastout")
+ lambda w: expand("blast.split/{id}.blastout",id=get_output_Profiles_splitProtFasta(w))
output:
"all.blastout"
shell:
@@ -144,7 +192,7 @@ rule Profiles_blastAll:
threads:
12
shell:
- "module load blast+/2.6.0 && blastp -query {input.fasta} -db {input.bank} -out {output} -outfmt 6 -num_threads {threads}"
+ "blastp -query {input.fasta} -db {input.bank} -out {output} -outfmt 6 -num_threads {threads}"
@@ -154,7 +202,7 @@ rule Profiles_makeBlastDB:
output:
"{part}.fasta.pin"
shell:
- "module load blast+/2.6.0 && makeblastdb -in {input} -dbtype prot"
+ "makeblastdb -in {input} -dbtype prot"
rule origNucl:
input:
@@ -162,13 +210,13 @@ rule origNucl:
output:
"nucl.fasta"
shell:
- "cp {input} {output}"
+ "gunzip -c {input} > {output}"
-rule ConvProt_splitInNames:
+checkpoint ConvProt_splitInNames:
input:
"nucl.fasta"
output:
- dynamic("nucl/part_{dataset}.names")
+ directory("nucl")
params:
chunkSize=10000
run:
@@ -182,28 +230,34 @@ rule ConvProt_splitInNames:
totalSeqs = len(seqNames)
print("Read {} sequence names from nucl.fasta.".format(totalSeqs))
nbChunks = round(totalSeqs / params["chunkSize"])
+ shell("mkdir {output}")
for i in range(nbChunks):
last = round((i+1)*(totalSeqs/nbChunks))
first = round(i*(totalSeqs/nbChunks))
- with open("nucl/part_{dataset}.names".format(dataset=i),"w") as o:
+ with open(f"{output}/{i}.names","w") as o:
for l in seqNames[first:(totalSeqs if i == (nbChunks-1) else last)]:
o.write(l+"\n")
-
+
+def get_output_ConvProt_splitInNames(w):
+ odir = checkpoints.ConvProt_splitInNames.get(**w).output[0]
+ return glob_wildcards(os.path.join(odir, "{i}.names")).i
+
+
rule ConvProt_goldenPart:
input:
- "nucl/part_{part}.names"
+ "nucl/{part}.names"
output:
- fasta="prot/part_{part}.fasta",
- incl="prot/part_{part}.fasta_included.txt",
- excl="prot/part_{part}.fasta_excluded.txt"
+ fasta="prot/{part}.fasta",
+ incl="prot/{part}.fasta_included.txt",
+ excl="prot/{part}.fasta_excluded.txt"
run:
- shell("module load golden/3.4.1 && python3 {workflow.basedir}/../build/nucl2ProtGolden.py {input} {output.fasta}")
+ shell("python3 {workflow.basedir}/../build/nucl2ProtGolden.py {input} {output.fasta}")
rule ConvProt_mergeFasta:
input:
- fasta=dynamic("prot/part_{dataset}.fasta"),
- incl=dynamic("prot/part_{dataset}.fasta_included.txt"),
- excl=dynamic("prot/part_{dataset}.fasta_excluded.txt")
+ fasta=lambda w: expand("prot/{i}.fasta",i=get_output_ConvProt_splitInNames(w)),
+ incl=lambda w: expand("prot/{i}.fasta_included.txt",i=get_output_ConvProt_splitInNames(w)),
+ excl=lambda w: expand("prot/{i}.fasta_excluded.txt",i=get_output_ConvProt_splitInNames(w)),
output:
fasta="prot.fasta",
incl="included.txt",
diff --git a/slurm.json b/slurm.json
index b7190bbbc7966069ca5f05dbb0b42487401f498d..cf6e05c990386658d2a8edc6355bc99e8a23d9cc 100644
--- a/slurm.json
+++ b/slurm.json
@@ -1,12 +1,31 @@
{
"__default__" :
{
- "partition" : "common",
- "qos" : "normal",
- "mem" : "3G",
- "extra" : "",
- "name" : "{jobname}.{rule}.{wildcards.part}",
- "out" : "logs/cluster/{rule}.{wildcards}.out",
- "error" : "logs/cluster/{rule}.{wildcards}.err"
+ "partition" : "dedicated,common",
+ "qos" : "fast",
+ "mem" : "3G",
+ "extra" : "",
+ "name" : "{sampleName}.{rule}.{wildcards.part}",
+ "out" : "logs/cluster/{rule}.{wildcards}.out",
+ "error" : "logs/cluster/{rule}.{wildcards}.err"
+ },
+ "Profiles_align" :
+ {
+ "name" : "{sampleName}.Profiles_align",
+ "qos" : "normal",
+ "partition" : "common",
+ "mem": "60000"
+ },
+ "Profiles_collapse" :
+ {
+ "name" : "{sampleName}.Profiles_collapse",
+ "mem" : "10G",
+ "qos" : "hubbioit",
+ "partition" : "hubbioit"
+ },
+ "Profiles_family_against_ref" :
+ {
+ "qos" : "normal",
+ "partition" : "common"
},
}