From 0c1bbd59bbd87b6e99b36d4b17b91f841a162406 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 15:37:08 +0200
Subject: [PATCH] Kallisto: update nf structure
---
src/nf_modules/Kallisto/indexing.config | 26 ++++
.../Kallisto/{tests/index.nf => indexing.nf} | 3 +-
src/nf_modules/Kallisto/kallisto.nf | 123 ------------------
...{kallisto.config => mapping_paired.config} | 14 --
.../Kallisto/{tests => }/mapping_paired.nf | 0
src/nf_modules/Kallisto/mapping_single.config | 26 ++++
.../Kallisto/{tests => }/mapping_single.nf | 0
src/nf_modules/Kallisto/{tests => }/tests.sh | 12 +-
8 files changed, 60 insertions(+), 144 deletions(-)
create mode 100644 src/nf_modules/Kallisto/indexing.config
rename src/nf_modules/Kallisto/{tests/index.nf => indexing.nf} (83%)
delete mode 100644 src/nf_modules/Kallisto/kallisto.nf
rename src/nf_modules/Kallisto/{kallisto.config => mapping_paired.config} (57%)
rename src/nf_modules/Kallisto/{tests => }/mapping_paired.nf (100%)
create mode 100644 src/nf_modules/Kallisto/mapping_single.config
rename src/nf_modules/Kallisto/{tests => }/mapping_single.nf (100%)
rename src/nf_modules/Kallisto/{tests => }/tests.sh (50%)
diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config
new file mode 100644
index 00000000..94c14cd2
--- /dev/null
+++ b/src/nf_modules/Kallisto/indexing.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "kallisto:0.44.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Kallisto/0.44.0"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/Kallisto/tests/index.nf b/src/nf_modules/Kallisto/indexing.nf
similarity index 83%
rename from src/nf_modules/Kallisto/tests/index.nf
rename to src/nf_modules/Kallisto/indexing.nf
index cae4bb03..9e38260f 100644
--- a/src/nf_modules/Kallisto/tests/index.nf
+++ b/src/nf_modules/Kallisto/indexing.nf
@@ -17,11 +17,12 @@ process index_fasta {
output:
file "*.index*" into index_files
+ file "*_kallisto_report.txt" into index_files_report
script:
"""
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
+2> ${fasta.baseName}_kallisto_report.txt
"""
}
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
deleted file mode 100644
index ae6b6b71..00000000
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
-* Kallisto :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/* fasta indexing */
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .set { fasta_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
-
- output:
- file "*.index*" into index_files
-
- script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-Channel
- .fromPath( params.index )
- .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
- .set { index_files }
-
-process mapping_fastq {
- tag "$reads"
- cpus 4
- publishDir "results/mapping/quantification/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*" into counts_files
-
- script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
-"""
-}
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 200
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-Channel
- .fromPath( params.index )
- .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
- .set { index_files }
-
-process mapping_fastq {
- tag "$file_id"
- cpus 4
- publishDir "results/mapping/quantification/", mode: 'copy'
-
- input:
- set file_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*" into count_files
-
- script:
-"""
-mkdir ${file_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
---bias --bootstrap-samples 100 -o ${file_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} > ${file_id}_kallisto_report.txt
-"""
-}
-
-
diff --git a/src/nf_modules/Kallisto/kallisto.config b/src/nf_modules/Kallisto/mapping_paired.config
similarity index 57%
rename from src/nf_modules/Kallisto/kallisto.config
rename to src/nf_modules/Kallisto/mapping_paired.config
index da7f54e0..de674527 100644
--- a/src/nf_modules/Kallisto/kallisto.config
+++ b/src/nf_modules/Kallisto/mapping_paired.config
@@ -3,9 +3,6 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
- container = "kallisto:0.44.0"
- }
$mapping_fastq {
container = "kallisto:0.44.0"
}
@@ -13,17 +10,6 @@ profiles {
}
sge {
process{
- $index_fasta {
- beforeScript = "module purge; module load Kallisto/0.44.0"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
$mapping_fastq {
beforeScript = "module purge; module load Kallisto/0.44.0"
executor = "sge"
diff --git a/src/nf_modules/Kallisto/tests/mapping_paired.nf b/src/nf_modules/Kallisto/mapping_paired.nf
similarity index 100%
rename from src/nf_modules/Kallisto/tests/mapping_paired.nf
rename to src/nf_modules/Kallisto/mapping_paired.nf
diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config
new file mode 100644
index 00000000..de674527
--- /dev/null
+++ b/src/nf_modules/Kallisto/mapping_single.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $mapping_fastq {
+ container = "kallisto:0.44.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $mapping_fastq {
+ beforeScript = "module purge; module load Kallisto/0.44.0"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/Kallisto/tests/mapping_single.nf b/src/nf_modules/Kallisto/mapping_single.nf
similarity index 100%
rename from src/nf_modules/Kallisto/tests/mapping_single.nf
rename to src/nf_modules/Kallisto/mapping_single.nf
diff --git a/src/nf_modules/Kallisto/tests/tests.sh b/src/nf_modules/Kallisto/tests.sh
similarity index 50%
rename from src/nf_modules/Kallisto/tests/tests.sh
rename to src/nf_modules/Kallisto/tests.sh
index f83a4cac..ec20292e 100755
--- a/src/nf_modules/Kallisto/tests/tests.sh
+++ b/src/nf_modules/Kallisto/tests.sh
@@ -1,16 +1,16 @@
-nextflow src/nf_modules/Kallisto/tests/index.nf \
- -c src/nf_modules/Kallisto/kallisto.config \
+nextflow src/nf_modules/Kallisto/indexing.nf \
+ -c src/nf_modules/Kallisto/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-nextflow src/nf_modules/Kallisto/tests/mapping_single.nf \
- -c src/nf_modules/Kallisto/kallisto.config \
+nextflow src/nf_modules/Kallisto/mapping_single.nf \
+ -c src/nf_modules/Kallisto/mapping_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-nextflow src/nf_modules/Kallisto/tests/mapping_paired.nf \
- -c src/nf_modules/Kallisto/kallisto.config \
+nextflow src/nf_modules/Kallisto/mapping_paired.nf \
+ -c src/nf_modules/Kallisto/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
--
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