From 67c4ff01fa733a562f16ceb7db3fcb4ab88f34a7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 16:54:02 +0200
Subject: [PATCH] SAMtools: update nf structure
---
src/nf_modules/SAMtools/filter_bams.config | 18 +++
.../SAMtools/{tests => }/filter_bams.nf | 9 +-
src/nf_modules/SAMtools/index_bams.config | 18 +++
.../SAMtools/{tests => }/index_bams.nf | 10 +-
src/nf_modules/SAMtools/samtools.config | 36 ------
src/nf_modules/SAMtools/samtools.nf | 117 ------------------
src/nf_modules/SAMtools/sort_bams.config | 18 +++
.../SAMtools/{tests => }/sort_bams.nf | 9 +-
src/nf_modules/SAMtools/split_bams.config | 18 +++
src/nf_modules/SAMtools/split_bams.nf | 27 ++++
src/nf_modules/SAMtools/tests.sh | 20 +++
src/nf_modules/SAMtools/tests/split_bams.nf | 26 ----
src/nf_modules/SAMtools/tests/tests.sh | 20 ---
13 files changed, 136 insertions(+), 210 deletions(-)
create mode 100644 src/nf_modules/SAMtools/filter_bams.config
rename src/nf_modules/SAMtools/{tests => }/filter_bams.nf (67%)
create mode 100644 src/nf_modules/SAMtools/index_bams.config
rename src/nf_modules/SAMtools/{tests => }/index_bams.nf (63%)
delete mode 100644 src/nf_modules/SAMtools/samtools.config
delete mode 100644 src/nf_modules/SAMtools/samtools.nf
create mode 100644 src/nf_modules/SAMtools/sort_bams.config
rename src/nf_modules/SAMtools/{tests => }/sort_bams.nf (53%)
create mode 100644 src/nf_modules/SAMtools/split_bams.config
create mode 100644 src/nf_modules/SAMtools/split_bams.nf
create mode 100755 src/nf_modules/SAMtools/tests.sh
delete mode 100644 src/nf_modules/SAMtools/tests/split_bams.nf
delete mode 100755 src/nf_modules/SAMtools/tests/tests.sh
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
new file mode 100644
index 0000000..0666840
--- /dev/null
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $filter_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $filter_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/SAMtools/tests/filter_bams.nf b/src/nf_modules/SAMtools/filter_bams.nf
similarity index 67%
rename from src/nf_modules/SAMtools/tests/filter_bams.nf
rename to src/nf_modules/SAMtools/filter_bams.nf
index 4902136..0812a19 100644
--- a/src/nf_modules/SAMtools/tests/filter_bams.nf
+++ b/src/nf_modules/SAMtools/filter_bams.nf
@@ -7,6 +7,7 @@ log.info "bed file : ${params.bed}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bam_files }
Channel
.fromPath( params.bed )
@@ -14,18 +15,18 @@ Channel
.set { bed_files }
process filter_bam {
- tag "$bam.baseName"
+ tag "$file_id"
cpus 4
input:
- file bam from bam_files
+ set file_id, file(bam) from bam_files
file bed from bed_files
output:
- file "*_filtered.bam*" into filtered_bam_files
+ set file_id, "*_filtered.bam*" into filtered_bam_files
script:
"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${file_id}_filtered.bam
"""
}
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
new file mode 100644
index 0000000..3b23601
--- /dev/null
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/SAMtools/tests/index_bams.nf b/src/nf_modules/SAMtools/index_bams.nf
similarity index 63%
rename from src/nf_modules/SAMtools/tests/index_bams.nf
rename to src/nf_modules/SAMtools/index_bams.nf
index bea5441..489b0f4 100644
--- a/src/nf_modules/SAMtools/tests/index_bams.nf
+++ b/src/nf_modules/SAMtools/index_bams.nf
@@ -5,14 +5,18 @@ log.info "bams files : ${params.bam}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bam_files }
process index_bam {
- tag "$bam.baseName"
+ tag "$file_id"
+
input:
- file bam from bam_files
+ set file_id, file(bam) from bam_files
+
output:
- file "*bam*" into indexed_bam_file
+ set file_id, "*.bam*" into indexed_bam_file
+
script:
"""
samtools index ${bam}
diff --git a/src/nf_modules/SAMtools/samtools.config b/src/nf_modules/SAMtools/samtools.config
deleted file mode 100644
index 001a77a..0000000
--- a/src/nf_modules/SAMtools/samtools.config
+++ /dev/null
@@ -1,36 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $sort_bam {
- container = "samtools:1.7"
- }
- $index_bam {
- container = "samtools:1.7"
- }
- $split_bam {
- container = "samtools:1.7"
- }
- $filter_bam {
- container = "samtools:1.7"
- }
- }
- }
- sge {
- process{
- $sort_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
- }
- $index_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
- }
- $split_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
- }
- $filter_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
- }
- }
- }
-}
diff --git a/src/nf_modules/SAMtools/samtools.nf b/src/nf_modules/SAMtools/samtools.nf
deleted file mode 100644
index f178bb0..0000000
--- a/src/nf_modules/SAMtools/samtools.nf
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
-* SAMtools :
-* Imputs : bam files
-* Output : bam files
-*/
-
-/* bams sorting */
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .set { bam_files }
-
-process sort_bam {
- tag "$bam.baseName"
- cpus 4
-
- input:
- file bam from bam_files
-
- output:
- file "*_sorted.bam" into sorted_bam_files
-
- script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
-"""
-}
-
-/* bams indexing */
-
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .set { bam_files }
-
-process index_bam {
- tag "$bam.baseName"
- input:
- file bam from bam_files
- output:
- file "*bam*" into indexed_bam_file
- script:
-"""
-samtools index ${bam}
-"""
-}
-
-
-/* bams spliting */
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .set { bam_files }
-
-process split_bam {
- tag "$bam.baseName"
- cpus 2
-
- input:
- file bam from bam_files
-
- output:
- file "*_forward.bam*" into forward_bam_files
- file "*_reverse.bam*" into reverse_bam_files
- script:
-"""
-samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
-"""
-}
-
-
-/* bams filtering */
-params.bam = "$baseDir/data/bam/*.bam"
-params.bed = "$baseDir/data/bam/*.bed"
-
-log.info "bams files : ${params.bam}"
-log.info "bed file : ${params.bed}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .set { bam_files }
-Channel
- .fromPath( params.bed )
- .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
- .set { bed_files }
-
-process filter_bam {
- tag "$bam.baseName"
- cpus 4
-
- input:
- file bam from bam_files
- file bed from bed_files
-
- output:
- file "*_filtered.bam*" into filtered_bam_files
- script:
-"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
-"""
-}
-
-
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
new file mode 100644
index 0000000..d1a8c50
--- /dev/null
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $sort_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $sort_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/SAMtools/tests/sort_bams.nf b/src/nf_modules/SAMtools/sort_bams.nf
similarity index 53%
rename from src/nf_modules/SAMtools/tests/sort_bams.nf
rename to src/nf_modules/SAMtools/sort_bams.nf
index 79a7590..ab5c7e5 100644
--- a/src/nf_modules/SAMtools/tests/sort_bams.nf
+++ b/src/nf_modules/SAMtools/sort_bams.nf
@@ -5,21 +5,22 @@ log.info "bams files : ${params.bam}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bam_files }
process sort_bam {
- tag "$bams.baseName"
+ tag "$file_id"
cpus 4
input:
- file bam from bam_files
+ set file_id, file(bam) from bam_files
output:
- file "*_sorted.bam" into sorted_bam_files
+ set file_id, "*_sorted.bam" into sorted_bam_files
script:
"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
"""
}
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
new file mode 100644
index 0000000..28b548e
--- /dev/null
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -0,0 +1,18 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $split_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $split_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/SAMtools/split_bams.nf b/src/nf_modules/SAMtools/split_bams.nf
new file mode 100644
index 0000000..f8ba6a5
--- /dev/null
+++ b/src/nf_modules/SAMtools/split_bams.nf
@@ -0,0 +1,27 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+ .fromPath( params.bam )
+ .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bam_files }
+
+process split_bam {
+ tag "$file_id"
+ cpus 2
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ set file_id, "*_forward.bam*" into forward_bam_files
+ set file_id, "*_reverse.bam*" into reverse_bam_files
+ script:
+"""
+samtools view -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
+"""
+}
+
diff --git a/src/nf_modules/SAMtools/tests.sh b/src/nf_modules/SAMtools/tests.sh
new file mode 100755
index 0000000..99a7ff3
--- /dev/null
+++ b/src/nf_modules/SAMtools/tests.sh
@@ -0,0 +1,20 @@
+nextflow src/nf_modules/SAMtools/sort_bams.nf \
+ -c src/nf_modules/SAMtools/sort_bams.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2.bam"
+
+nextflow src/nf_modules/SAMtools/index_bams.nf \
+ -c src/nf_modules/SAMtools/index_bams.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+
+nextflow src/nf_modules/SAMtools/split_bams.nf \
+ -c src/nf_modules/SAMtools/split_bams.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2.bam"
+
+nextflow src/nf_modules/SAMtools/filter_bams.nf \
+ -c src/nf_modules/SAMtools/filter_bams.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ --bed "data/tiny_dataset/OLD/2genes.bed"
diff --git a/src/nf_modules/SAMtools/tests/split_bams.nf b/src/nf_modules/SAMtools/tests/split_bams.nf
deleted file mode 100644
index edc2086..0000000
--- a/src/nf_modules/SAMtools/tests/split_bams.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .set { bam_files }
-
-process split_bam {
- tag "$bam.baseName"
- cpus 2
-
- input:
- file bam from bam_files
-
- output:
- file "*_forward.bam*" into forward_bam_files
- file "*_reverse.bam*" into reverse_bam_files
- script:
-"""
-samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
-"""
-}
-
diff --git a/src/nf_modules/SAMtools/tests/tests.sh b/src/nf_modules/SAMtools/tests/tests.sh
deleted file mode 100755
index e3e8099..0000000
--- a/src/nf_modules/SAMtools/tests/tests.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-nextflow src/nf_modules/SAMtools/tests/sort_bams.nf \
- -c src/nf_modules/SAMtools/samtools.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-nextflow src/nf_modules/SAMtools/tests/index_bams.nf \
- -c src/nf_modules/SAMtools/samtools.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-
-nextflow src/nf_modules/SAMtools/tests/split_bams.nf \
- -c src/nf_modules/SAMtools/samtools.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
-
-nextflow src/nf_modules/SAMtools/tests/filter_bams.nf \
- -c src/nf_modules/SAMtools/samtools.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- --bed "data/tiny_dataset/OLD/2genes.bed"
--
GitLab