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Update pipeline to IPSA 4.0 workflow
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@emi80
emi80 committed May 31, 2017
1 parent 151649e commit 330054f
Showing 1 changed file with 62 additions and 100 deletions.
162 changes: 62 additions & 100 deletions ipsa.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@ params.deltaSS = 10
params.dir = 'data'
params.entropy = 1.5
params.group = 'labExpId'
params.idr = 0.1
params.margin = 5
params.merge = "all"
params.mincount = 10
Expand Down Expand Up @@ -41,7 +40,6 @@ if (params.help) {
log.info '--dir DIRECTORY the output directory, obligatory'
log.info '--entropy ENTROPY entropy lower threshold, default=1.5'
log.info '--group GROUP the grouping field for IDR, default=labExpId'
log.info '--idr IDR IDR upper threshold, default=0.1'
log.info '--margin MARGIN margin for aggregate, default=5'
log.info '--merge MERGE the name of the output to merge in case if blocks are missing, default=all'
log.info '--mincount MIN_COUNT min number of counts for the denominator, default=10'
Expand Down Expand Up @@ -74,7 +72,6 @@ log.info "Splice sites distance threshold : ${params.deltaSS}"
log.info "Output dir : ${params.dir}"
log.info "Entropy lowewr threshold : ${params.entropy}"
log.info "Grouping field : ${params.group}"
log.info "IDR upper threshold : ${params.idr}"
log.info "Margin for aggregate : ${params.margin}"
log.info "Merge output name : ${params.merge}"
log.info "Minimum counts for denominator : ${params.mincount}"
Expand Down Expand Up @@ -149,13 +146,13 @@ process sjcount {
set sample, id, file(bam), type, view, readType, readStrand, readLength from bamsWreadLength

output:
set id, val(1), file("${prefix}.A01.ssj.tsv"), readLength into A01ssc
set id, val(0), file("${prefix}.A01.ssc.tsv"), readLength into A01ssj
set id, val(2), file("${prefix}.A01.ssj.tsv") into A01mex
set id, file("${prefix}.ssc.tsv"), readLength into A01ssc
set id, file("${prefix}.ssj.tsv"), readLength into A01ssj
set id, file("${prefix}.ssj.tsv") into A01mex

script:
endpoint = 'A01'
prefix = bam.name.replace(/.bam/,'')
prefix = "${id}.${endpoint}"
def strandParams
switch (readStrand) {
case'SENSE':
Expand All @@ -173,30 +170,50 @@ process sjcount {
}
"""
sjcount -bam ${bam} \
-ssc ${prefix}.A01.ssc.tsv \
-ssj ${prefix}.A01.ssj.tsv \
-ssc ${prefix}.ssc.tsv \
-ssj ${prefix}.ssj.tsv \
-nbins ${readLength} \
${strandParams} \
${params.param ?: ''} \
-quiet
"""
}

process aggregate {
process aggregateSSC {

publishDir "${params.dir}/${endpoint}"

input:
set id, file(tsv), readLength from A01ssc

output:
set id, file("${prefix}.tsv") into sscA02

script:
degree = 0
endpoint = 'A02'
prefix = "${id}.${endpoint}.ssc"
"""
aggregate.awk -v degree=${degree} -v readLength=${readLength} -v margin=${params.margin} -v prefix= -v logfile=${prefix}.log ${tsv} > ${prefix}.tsv
"""
}

process aggregateSSJ {

publishDir "${params.dir}/${endpoint}"

input:
set id, splits, file(tsv), readLength from A01ssc.mix(A01ssj)
set id, file(tsv), readLength from A01ssj

output:
set id, file("${prefix}.tsv") into A02
set id, file("${prefix}.tsv") into ssjA02

script:
degree = 1
endpoint = 'A02'
prefix = tsv.name.replace(/.tsv/,'').replace(/A01/,'A02')
prefix = "${id}.${endpoint}.ssj"
"""
awk '\$2==${splits}' ${tsv} | agg.pl -readLength ${readLength} -margin ${params.margin} -logfile ${prefix}.log > ${prefix}.tsv
aggregate.awk -v degree=${degree} -v readLength=${readLength} -v margin=${params.margin} -v prefix= -v logfile=${prefix}.log ${tsv} > ${prefix}.tsv
"""
}

Expand All @@ -205,7 +222,7 @@ process aggregateMex {
publishDir "${params.dir}/${endpoint}"

input:
set id, splits, file(tsv) from A01mex
set id, file(tsv) from A01mex

when:
params.microexons
Expand All @@ -214,21 +231,14 @@ process aggregateMex {
set id, file("${prefix}.tsv") into D01

script:
degree = 2
endpoint = 'D01'
prefix = tsv.name.replace(/.tsv/,'').replace(/A01.ssj/,'D01')
"""
awk '\$2==${splits}' ${tsv} | agg.pl -logfile ${prefix}.log > ${prefix}.tsv
aggregate.awk -v degree=${degree} -v logfile=${prefix}.log ${tsv} > ${prefix}.tsv
"""
}

Channel.create().set { sscA02 }
Channel.create().set { ssjA02 }

A02.choice(sscA02, ssjA02) {
f = it[1]
f.name =~ /ssc/ ? 0 : 1
}

process annotate {

publishDir "${params.dir}/${endpoint}"
Expand All @@ -243,7 +253,7 @@ process annotate {

script:
endpoint = 'A03'
prefix = ssj.name.replace(/.tsv/,'').replace(/A02/,'A03')
prefix = "${id}.${endpoint}.ssj"
"""
annotate.pl -annot ${annotation} -dbx ${genomeDBX} -idx ${genomeIDX} -deltaSS ${params.deltaSS} -in ${ssj} > ${prefix}.tsv
"""
Expand All @@ -261,9 +271,9 @@ process chooseStrand {

script:
endpoint = 'A04'
prefix = ssj.name.replace(/.tsv/,'').replace(/A03/,'A04')
prefix = "${id}.${endpoint}.ssj"
"""
choose_strand.pl - < ${ssj} -logfile ${prefix}.log > ${prefix}.tsv
choose_strand.awk ${ssj} > ${prefix}.tsv
"""
}

Expand Down Expand Up @@ -294,9 +304,9 @@ process constrainSSC {

script:
endpoint = 'A04'
prefix = ssc.name.replace(/.tsv/,'').replace(/A02/,'A04')
prefix = "${id}.${endpoint}.ssc"
"""
constrain_ssc.pl -ssj ${ssj} < ${ssc} > ${prefix}.tsv
constrain_ssc.awk -v jncfile=${ssj} ${ssc} > ${prefix}.tsv
"""
}

Expand All @@ -312,9 +322,9 @@ process constrainMex {

script:
endpoint = 'D02'
prefix = ssjMex.name.replace(/.tsv/,'').replace(/D01/,'D02')
prefix = "${id}.${endpoint}"
"""
constrain_mult.pl -ssj ${ssj} < ${ssjMex} > ${prefix}.tsv
constrain_mex.awk -v jncfile=${ssj} ${ssjMex} > ${prefix}.tsv
"""
}

Expand All @@ -326,67 +336,32 @@ process extractMex {
set id, file(ssjMex) from D02

output:
set id, file("${prefix}.tsv") into D03
set id, file("${prefix}.tsv") into D06

script:
endpoint = 'D03'
prefix = ssjMex.name.replace(/.tsv/,'').replace(/D02/,'D03')
endpoint = 'D06'
prefix = "${id}.${endpoint}"
"""
extract_mex.pl < ${ssjMex} > ${prefix}.tsv
extract_mex.awk ${ssjMex} > ${prefix}.tsv
"""
}

process ssjIDR {
process sscA06 {

publishDir "${params.dir}/${endpoint}"

input:
set id, file(tsv) from ssjA04

output:
set id, file("${prefix}.tsv") into ssjA05

script:
endpoint = 'A05'
prefix = "${id}.${endpoint}.ssj"
"""
idr4sj.pl ${tsv} > ${prefix}.tsv
"""
}

process sscIDR {

publishDir "${params.dir}/${endpoint}"

input:
set id, file(tsv) from sscA04
set id, file(ssc) from sscA04

output:
set id, file("${prefix}.tsv") into sscA05
file "${prefix}.tsv" into sscA06
set id, file("${prefix}.tsv") into ssc4merge, ssc4allA06

script:
endpoint = 'A05'
endpoint = 'A06'
prefix = "${id}.${endpoint}.ssc"
"""
idr4sj.pl ${tsv} > ${prefix}.tsv
"""
}

process idrMex {

publishDir "${params.dir}/${endpoint}"

input:
set id, file(tsv) from D03

output:
set id, file("${prefix}.tsv") into D06

script:
endpoint = 'D06'
prefix = "${id}.${endpoint}.mex"
"""
idr4sj.pl ${tsv} > ${prefix}.tsv
awk '\$4>=${params.entropy}' ${ssc} > ${prefix}.tsv
"""
}

Expand All @@ -395,36 +370,17 @@ process ssjA06 {
publishDir "${params.dir}/${endpoint}"

input:
set id, file(ssj) from ssjA05
set id, file(ssj) from ssjA04

output:
file "${prefix}.tsv" into ssjA06, ssj4gffA06
set id, file("${prefix}.tsv") into ssj4merge, ssj4allA06, ssj4psicasA06

script:
endpoint = 'A06'
prefix = ssj.name.replace(/.tsv/,'').replace(/A05/,'A06')
"""
awk '\$4>=${params.entropy} && \$5>=${params.status} && \$7<${params.idr}' ${ssj} > ${prefix}.tsv
"""
}

process sscA06 {

publishDir "${params.dir}/${endpoint}"

input:
set id, file(ssc) from sscA05

output:
file "${prefix}.tsv" into sscA06
set id, file("${prefix}.tsv") into ssc4merge, ssc4allA06

script:
endpoint = 'A06'
prefix = ssc.name.replace(/.tsv/,'').replace(/A05/,'A06')
prefix = "${id}.${endpoint}.ssj"
"""
awk '\$4>=${params.entropy} && \$7<${params.idr}' ${ssc} > ${prefix}.tsv
awk '\$4>=${params.entropy} && \$5>=${params.status}' ${ssj} > ${prefix}.tsv
"""
}

Expand Down Expand Up @@ -587,14 +543,19 @@ process mergeGFFzeta {
file "${prefix}.psi.tsv"
file "${prefix}.psi3.tsv"
file "${prefix}.psi5.tsv"
file "${prefix}.psit.tsv"
file "${prefix}.cosi.tsv"
file "${prefix}.cosi3.tsv"
file "${prefix}.cosi5.tsv"
file "${prefix}.cosit.tsv"
file "${prefix}.exc.tsv"
file "${prefix}.inc.tsv"
file "${prefix}.ret.tsv"

shell:
prefix = "${params.merge}.A"
input = [sscs.toList(), ids].transpose().flatten().collect { "'$it'" }.join(',')
features = ['cosi', 'cosi3', 'cosi5', 'psi', 'psi3', 'psi5']
features = ['cosi', 'cosi3', 'cosi5', 'cosit', 'psi', 'psi3', 'psi5', 'psit', 'exc', 'inc', 'ret']
output = features.collect { "'${it}', '${prefix}.${it}.tsv'" }.join(',')
percent = 0.25
transf = 'log'
Expand All @@ -609,11 +570,12 @@ process mergeGFFpsicas {

output:
file "${prefix}.psicas.tsv"
file "${prefix}.psiloc.tsv"

shell:
prefix = "${params.merge}.B"
input = [sscs.toList(), ids].transpose().flatten().collect { "'$it'" }.join(',')
features = ['psicas']
features = ['psicas', 'psiloc']
output = features.collect { "'${it}', '${prefix}.${it}.tsv'" }.join(',')
percent = 0.25
transf = 'log'
Expand Down

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