From 292c183a6552d53ca8a6f2b1fc6c91d56459e447 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Thu, 19 Mar 2020 11:17:18 +0100
Subject: [PATCH] add
src/nf_modules/stringtie/transcriptome_{sohrt,long}Reads.nf
---
.../stringtie/transcriptome_longReads.config | 12 +++++++
.../stringtie/transcriptome_longReads.nf | 33 +++++++++++++++++++
.../stringtie/transcriptome_shortReads.nf | 32 ++++++++++++++++++
3 files changed, 77 insertions(+)
create mode 100644 src/nf_modules/stringtie/transcriptome_longReads.config
create mode 100644 src/nf_modules/stringtie/transcriptome_longReads.nf
create mode 100644 src/nf_modules/stringtie/transcriptome_shortReads.nf
diff --git a/src/nf_modules/stringtie/transcriptome_longReads.config b/src/nf_modules/stringtie/transcriptome_longReads.config
new file mode 100644
index 00000000..1a385c7e
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_longReads.config
@@ -0,0 +1,12 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: stringtie {
+ cpus = 1
+ container = "informationsea/stringtie:2.1.1"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/stringtie/transcriptome_longReads.nf b/src/nf_modules/stringtie/transcriptome_longReads.nf
new file mode 100644
index 00000000..e0ba8bd2
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_longReads.nf
@@ -0,0 +1,33 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.bam )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bam_files }
+
+///////////////////////////////////////////////////////////////////////////////
+// TRANSCRIPTOME BUILDING
+
+process stringtie {
+ tag "$file_id"
+ publishDir "results/stringtie/${file_id}", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ file "*.gtf" into gtf_transcriptome
+
+ script:
+ """
+stringtie -L \
+ -o ${file_id}.gtf \
+ -f 0.001 \
+ -j 0.5 ${bam}
+ """
+}
+
+// END STRNGTIE
diff --git a/src/nf_modules/stringtie/transcriptome_shortReads.nf b/src/nf_modules/stringtie/transcriptome_shortReads.nf
new file mode 100644
index 00000000..68ad9999
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_shortReads.nf
@@ -0,0 +1,32 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.bam )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bam_files }
+
+///////////////////////////////////////////////////////////////////////////////
+// TRANSCRIPTOME BUILDING
+
+process stringtie {
+ tag "$file_id"
+ publishDir "results/stringtie/${file_id}", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ file "*.gtf" into gtf_files
+
+ script:
+ """
+stringtie -o ${file_id}.gtf \
+ -f 0.01 \
+ -j 0.5 ${bam}
+ """
+}
+
+// END STRNGTIE
--
GitLab