From 4afb198104499ea211dd29c2fdd7de8bcfecccb4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 14:14:08 +0200
Subject: [PATCH] Bowtie: update nf structure
---
src/nf_modules/Bowtie/bowtie.nf | 138 ------------------
src/nf_modules/Bowtie/indexing.config | 18 +++
.../Bowtie/{tests/index.nf => indexing.nf} | 2 +
.../{bowtie.config => mapping_paired.config} | 6 -
.../Bowtie/{tests => }/mapping_paired.nf | 4 +
src/nf_modules/Bowtie/mapping_single.config | 18 +++
.../Bowtie/{tests => }/mapping_single.nf | 4 +
src/nf_modules/Bowtie/{tests => }/tests.sh | 12 +-
8 files changed, 52 insertions(+), 150 deletions(-)
delete mode 100644 src/nf_modules/Bowtie/bowtie.nf
create mode 100644 src/nf_modules/Bowtie/indexing.config
rename src/nf_modules/Bowtie/{tests/index.nf => indexing.nf} (89%)
rename src/nf_modules/Bowtie/{bowtie.config => mapping_paired.config} (66%)
rename src/nf_modules/Bowtie/{tests => }/mapping_paired.nf (97%)
create mode 100644 src/nf_modules/Bowtie/mapping_single.config
rename src/nf_modules/Bowtie/{tests => }/mapping_single.nf (97%)
rename src/nf_modules/Bowtie/{tests => }/tests.sh (50%)
diff --git a/src/nf_modules/Bowtie/bowtie.nf b/src/nf_modules/Bowtie/bowtie.nf
deleted file mode 100644
index 0344760..0000000
--- a/src/nf_modules/Bowtie/bowtie.nf
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
-* Bowtie :
-* 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 bam files matching: ${params.fasta}" }
- .set { fasta_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- cpus 4
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
-
- output:
- file "*.index*" into index_files
- file "*_report.txt" into indexing_report
-
- script:
-"""
-bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
- exit 1
-fi
-"""
-}
-
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$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: ${params.index}" }
- .set { index_files }
-
-process mapping_fastq {
- tag "$pair_id"
- cpus 4
- publishDir "results/mapping/bams/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*.bam" into bam_files
- file "*_report.txt" into mapping_report
-
- script:
- index_id = index[0]
- for (index_file in index) {
- if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
- index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
- }
- }
-"""
-# -v specify the max number of missmatch, -k the number of match reported per
-# reads
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie_report.txt; then
- exit 1
-fi
-"""
-}
-
-
-/*
-* for single-end data
-*/
-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/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
new file mode 100644
index 0000000..d585100
--- /dev/null
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "bowtie:1.2.2"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Bowtie/1.2.2"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/Bowtie/tests/index.nf b/src/nf_modules/Bowtie/indexing.nf
similarity index 89%
rename from src/nf_modules/Bowtie/tests/index.nf
rename to src/nf_modules/Bowtie/indexing.nf
index f9ee2eb..537d684 100644
--- a/src/nf_modules/Bowtie/tests/index.nf
+++ b/src/nf_modules/Bowtie/indexing.nf
@@ -1,3 +1,5 @@
+/* fasta indexing */
+
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
diff --git a/src/nf_modules/Bowtie/bowtie.config b/src/nf_modules/Bowtie/mapping_paired.config
similarity index 66%
rename from src/nf_modules/Bowtie/bowtie.config
rename to src/nf_modules/Bowtie/mapping_paired.config
index 93fe4a4..86cc4bb 100644
--- a/src/nf_modules/Bowtie/bowtie.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -3,9 +3,6 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
- container = "bowtie:1.2.2"
- }
$mapping_fastq {
container = "bowtie:1.2.2"
}
@@ -13,9 +10,6 @@ profiles {
}
sge {
process{
- $index_fasta {
- beforeScript = "module purge; module load Bowtie/1.2.2"
- }
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
}
diff --git a/src/nf_modules/Bowtie/tests/mapping_paired.nf b/src/nf_modules/Bowtie/mapping_paired.nf
similarity index 97%
rename from src/nf_modules/Bowtie/tests/mapping_paired.nf
rename to src/nf_modules/Bowtie/mapping_paired.nf
index 600e295..cc9f40b 100644
--- a/src/nf_modules/Bowtie/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie/mapping_paired.nf
@@ -1,3 +1,7 @@
+/*
+* mapping paired fastq
+*/
+
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
new file mode 100644
index 0000000..86cc4bb
--- /dev/null
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $mapping_fastq {
+ container = "bowtie:1.2.2"
+ }
+ }
+ }
+ sge {
+ process{
+ $mapping_fastq {
+ beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/Bowtie/tests/mapping_single.nf b/src/nf_modules/Bowtie/mapping_single.nf
similarity index 97%
rename from src/nf_modules/Bowtie/tests/mapping_single.nf
rename to src/nf_modules/Bowtie/mapping_single.nf
index 6697681..ad9754d 100644
--- a/src/nf_modules/Bowtie/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie/mapping_single.nf
@@ -1,3 +1,7 @@
+/*
+* mapping single end fastq
+*/
+
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
diff --git a/src/nf_modules/Bowtie/tests/tests.sh b/src/nf_modules/Bowtie/tests.sh
similarity index 50%
rename from src/nf_modules/Bowtie/tests/tests.sh
rename to src/nf_modules/Bowtie/tests.sh
index 3b67514..803f628 100755
--- a/src/nf_modules/Bowtie/tests/tests.sh
+++ b/src/nf_modules/Bowtie/tests.sh
@@ -1,16 +1,16 @@
-./nextflow src/nf_modules/Bowtie/tests/index.nf \
- -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/indexing.nf \
+ -c src/nf_modules/Bowtie/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-./nextflow src/nf_modules/Bowtie/tests/mapping_single.nf \
- -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/mapping_single.nf \
+ -c src/nf_modules/Bowtie/mapping_single.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-./nextflow src/nf_modules/Bowtie/tests/mapping_paired.nf \
- -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
+ -c src/nf_modules/Bowtie/mapping_paired.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
--
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