diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..ddf93b6ec57c876681fc508a737b3287e20fdd61
--- /dev/null
+++ b/src/nf_modules/RSEM/indexing.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "rsem:1.3.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/RSEM/tests/index.nf b/src/nf_modules/RSEM/indexing.nf
similarity index 100%
rename from src/nf_modules/RSEM/tests/index.nf
rename to src/nf_modules/RSEM/indexing.nf
diff --git a/src/nf_modules/RSEM/rsem.config b/src/nf_modules/RSEM/quantification_paired.config
similarity index 63%
rename from src/nf_modules/RSEM/rsem.config
rename to src/nf_modules/RSEM/quantification_paired.config
index 3209b6bcd480b36b1f5e48a1055db2cc8fc93e93..344ab1e30497454826a5e45537f0e8182fb8dc63 100644
--- a/src/nf_modules/RSEM/rsem.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -3,9 +3,6 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
- container = "rsem:1.3.0"
- }
$mapping_fastq {
container = "rsem:1.3.0"
}
@@ -13,9 +10,6 @@ profiles {
}
sge {
process{
- $index_fasta {
- beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
- }
$mapping_fastq {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
diff --git a/src/nf_modules/RSEM/tests/quantification_paired.nf b/src/nf_modules/RSEM/quantification_paired.nf
similarity index 68%
rename from src/nf_modules/RSEM/tests/quantification_paired.nf
rename to src/nf_modules/RSEM/quantification_paired.nf
index 0109500908f61159c5426b35c7dcb1a02fb60022..a22950fd2b4a0548ea7a45bc0a0965992246047f 100644
--- a/src/nf_modules/RSEM/tests/quantification_paired.nf
+++ b/src/nf_modules/RSEM/quantification_paired.nf
@@ -20,20 +20,29 @@ process mapping_fastq {
input:
set pair_id, file(reads) from fastq_files
- file index from index_files.collect()
+ file index from index_files.toList()
output:
file "*" into counts_files
script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
-output-genome-bam -p ${task.cpus} \
---paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
-> ${pair_id}_rsem_bowtie2_report.txt
+--paired-end ${reads[0]} ${reads[1]} ${index_id} ${pair_id} \
+2> ${pair_id}_rsem_bowtie2_report.txt
+
+if grep -q "Error" ${pair_id}_rsem_bowtie2_report.txt; then
+ exit 1
+fi
"""
}
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..344ab1e30497454826a5e45537f0e8182fb8dc63
--- /dev/null
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $mapping_fastq {
+ container = "rsem:1.3.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $mapping_fastq {
+ beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/RSEM/tests/quantification_single.nf b/src/nf_modules/RSEM/quantification_single.nf
similarity index 72%
rename from src/nf_modules/RSEM/tests/quantification_single.nf
rename to src/nf_modules/RSEM/quantification_single.nf
index 47e0047f7a1bbc53d629685ffe4166086cb14c35..d52b7f446049abac081b5a17f2202909f070e600 100644
--- a/src/nf_modules/RSEM/tests/quantification_single.nf
+++ b/src/nf_modules/RSEM/quantification_single.nf
@@ -1,6 +1,6 @@
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
-params.mean = 125
+params.mean = 200
params.sd = 100
log.info "fastq files : ${params.fastq}"
@@ -25,21 +25,31 @@ process mapping_fastq {
input:
set file_id, file(reads) from fastq_files
- file index from index_files.collect()
+ file index from index_files.toList()
output:
file "*" into count_files
script:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
+ls -l
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${file_id} \
-> ${reads.baseName}_rsem_bowtie2_report.txt
+${reads} ${index_id} ${file_id} \
+2> ${file_id}_rsem_bowtie2_report.txt
+
+if grep -q "Error" ${file_id}_rsem_bowtie2_report.txt; then
+ exit 1
+fi
"""
}
diff --git a/src/nf_modules/RSEM/rsem.nf b/src/nf_modules/RSEM/rsem.nf
deleted file mode 100644
index aa2fc957e8b547f23106b677692ea76501eeedc2..0000000000000000000000000000000000000000
--- a/src/nf_modules/RSEM/rsem.nf
+++ /dev/null
@@ -1,140 +0,0 @@
-/*
-* RSEM :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/* fasta indexing */
-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gff3"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .set { fasta_file }
-Channel
- .fromPath( params.annotation )
- .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
- .set { annotation_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- cpus 4
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
- file annotation from annotation_file
-
- output:
- file "*.index*" into index_files
-
- script:
- def cmd_annotation = "--gff3 ${annotation}"
- if(annotation ==~ /.*\.gtf$/){
- cmd_annotation = "--gtf ${annotation}"
- }
-"""
-rsem-prepare-reference -p ${task.cpus} --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
-${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
-${fasta.baseName}_rsem_bowtie2_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: ${params.index}" }
- .set { index_files }
-
-process mapping_fastq {
- tag "$pair_id"
- 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:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
--output-genome-bam -p ${task.cpus} \
---paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
-> ${pair_id}_rsem_bowtie2_report.txt
-"""
-}
-
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 125
-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:
-index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
---fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
---output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${file_id} \
-> ${reads.baseName}_rsem_bowtie2_report.txt
-"""
-}
diff --git a/src/nf_modules/RSEM/tests/tests.sh b/src/nf_modules/RSEM/tests.sh
similarity index 54%
rename from src/nf_modules/RSEM/tests/tests.sh
rename to src/nf_modules/RSEM/tests.sh
index f7fcd064b93430badd67899831561121580e4709..c57c8c4feff12d566cb2529651c23e90e7bbb919 100755
--- a/src/nf_modules/RSEM/tests/tests.sh
+++ b/src/nf_modules/RSEM/tests.sh
@@ -1,17 +1,17 @@
-nextflow src/nf_modules/RSEM/tests/index.nf \
- -c src/nf_modules/RSEM/rsem.config \
+nextflow src/nf_modules/RSEM/indexing.nf \
+ -c src/nf_modules/RSEM/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--annotation "data/tiny_dataset/annot/tiny.gff"
-nextflow src/nf_modules/RSEM/tests/quantification_single.nf \
- -c src/nf_modules/RSEM/rsem.config \
+nextflow src/nf_modules/RSEM/quantification_single.nf \
+ -c src/nf_modules/RSEM/quantification_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-nextflow src/nf_modules/RSEM/tests/quantification_paired.nf \
- -c src/nf_modules/RSEM/rsem.config \
+nextflow src/nf_modules/RSEM/quantification_paired.nf \
+ -c src/nf_modules/RSEM/quantification_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"