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LBMC
Delattre
kmer diff
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3ce8e9b0e62416fd69112f1fab88b03e34c80d60 to bcbb832e7cb62e9c156930197acd0675d7b58182
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main.nf: merge sample by sample and r1 r2
· 317649bd
Laurent Modolo
authored
1 year ago
Verified
317649bd
COLLATEKMER: ensure to have male / female columns
· bcbb832e
Laurent Modolo
authored
1 year ago
Verified
bcbb832e
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src/main.nf
+11
-2
11 additions, 2 deletions
src/main.nf
src/modules/mergekmer.nf
+2
-2
2 additions, 2 deletions
src/modules/mergekmer.nf
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13 additions
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4 deletions
src/main.nf
View file @
bcbb832e
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@@ -31,8 +31,17 @@ workflow {
SUBSAMPLE_READ(fastq.r1.mix(fastq.r2))
SPLIT(SUBSAMPLE_READ.out.fastq)
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.groupTuple())
COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
MERGEKMER(FASTKMERS.out.csv.map{it -> [[it[0][0], it[0][1], it[0][2]], it[1]]}.groupTuple())
COLLATEKMER(
MERGEKMER.out.csv
.filter{ it[0].sex == "male" }
.map{ it -> [it[0].specice, it[1]]}
.join(
MERGEKMER.out.csv
.filter{ it[0].sex == "female" }
.map{ it -> [it[0].specice, it[1]]}
)
)
KMERCLUST_LOAD(COLLATEKMER.out.csv, params_csv.collect())
KMERCLUST_BOOT(Channel.of(1..params.bootstrap).combine(KMERCLUST_LOAD.out.rdata))
KMERCLUST_CLUST(Channel.from(["XY", "XO", "OO"]).combine(KMERCLUST_LOAD.out.rdata))
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src/modules/mergekmer.nf
View file @
bcbb832e
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@@ -31,7 +31,7 @@ process COLLATEKMER {
container "lbmc/mergekmer:0.1.2"
input:
tuple val(specie), path(csv)
tuple val(specie), path(
male_csv), path(female_
csv)
output:
tuple val(specie), path("*.csv"), emit: csv
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@@ -40,7 +40,7 @@ process COLLATEKMER {
script:
def args = task.ext.args ?: ''
"""
mergekmer --csv ${csv} --output ${specie}.csv --collate
mergekmer --csv ${
male_csv} ${female_
csv} --output ${specie}.csv --collate
cat <<-END_VERSIONS > versions.yml
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