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Verified Commit 59ce096b authored by Laurent Modolo's avatar Laurent Modolo
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Merge branch 'master' of gitlab_lbmc:pipelines/nextflow

parents 6d8d8279 e98e98b6
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......@@ -5,7 +5,7 @@ You can fork this repository to build your own pipeline.
To get the last commits from this repository into your fork use the following commands:
```sh
git remote add upstream https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow.git
git remote add upstream gitlab_lbmc:pipelines/nextflow.git
git pull upstream master
```
......
......@@ -25,6 +25,7 @@ process index_fasta {
output:
file "*.index*" into index_files
file "*_report.txt" into indexing_report
script:
"""
......@@ -68,6 +69,7 @@ process mapping_fastq {
output:
file "*.bam" into bam_files
file "*_report.txt" into mapping_report
script:
index_id = index[0]
......@@ -119,6 +121,7 @@ process mapping_fastq {
output:
file "*.bam" into bam_files
file "*_report.txt" into mapping_report
script:
index_id = index[0]
......
......@@ -17,6 +17,7 @@ process index_fasta {
output:
file "*.index*" into index_files
file "*_report.txt" into indexing_report
script:
"""
......
......@@ -24,11 +24,12 @@ process mapping_fastq {
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/) {
if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
}
}
......
......@@ -23,17 +23,18 @@ process mapping_fastq {
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/) {
if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
}
}
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
-U ${reads} 2> \
-q ${reads} 2> \
${reads.baseName}_bowtie_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
......
......@@ -25,6 +25,7 @@ process index_fasta {
output:
file "*.index*" into index_files
file "*_report.txt" into indexing_report
script:
"""
......@@ -72,7 +73,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
......@@ -122,7 +123,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
......
......@@ -17,6 +17,7 @@ process index_fasta {
output:
file "*.index*" into index_files
file "*_report.txt" into indexing_report
script:
"""
......
......@@ -29,7 +29,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
......
......@@ -28,7 +28,7 @@ process mapping_fastq {
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
......
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