From ed5b2f4717d3fb7075bf41ac8833e9b944bf704e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 24 Jun 2021 10:52:10 +0200
Subject: [PATCH] docker: add htseq 0.13.5

---
 src/.docker_modules/htseq/0.13.5/Dockerfile     |  2 ++
 src/.docker_modules/htseq/0.13.5/docker_init.sh |  4 ++++
 src/nf_modules/kb/main.nf                       | 12 ++++++++++++
 3 files changed, 18 insertions(+)
 create mode 100644 src/.docker_modules/htseq/0.13.5/Dockerfile
 create mode 100755 src/.docker_modules/htseq/0.13.5/docker_init.sh

diff --git a/src/.docker_modules/htseq/0.13.5/Dockerfile b/src/.docker_modules/htseq/0.13.5/Dockerfile
new file mode 100644
index 00000000..68347cf4
--- /dev/null
+++ b/src/.docker_modules/htseq/0.13.5/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/htseq:0.13.5--py39h70b41aa_1
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/htseq/0.13.5/docker_init.sh b/src/.docker_modules/htseq/0.13.5/docker_init.sh
new file mode 100755
index 00000000..ca03fe9a
--- /dev/null
+++ b/src/.docker_modules/htseq/0.13.5/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/htseq:0.13.5
+docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5'
+docker push lbmc/htseq:0.13.5
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 6bb6d764..5110b222 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -147,6 +147,7 @@ process kb_default {
     -x 10XV3 \
     ${params.count} \
     ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
   """
 }
 
@@ -196,6 +197,7 @@ process kb_marseq {
     ${params.count} \
     -x 1,0,6:1,6,14:0,0,0 \
     ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
   """
   else
   """
@@ -209,6 +211,7 @@ process kb_marseq {
     ${params.count} \
     -x 1,0,6:1,6,14:0,0,0 \
     ${reads} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
   """
 }
 
@@ -335,6 +338,9 @@ process velocity_default {
     -x 10XV3 \
     ${params.count} \
     ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
+  cp ${cdna_t2g} ${file_prefix}/
+  cp ${intron_t2g} ${file_prefix}/
   """
 }
 
@@ -387,6 +393,9 @@ process velocity_marseq {
     ${params.count} \
     -x 1,0,6:1,6,14:0,0,0 \
     ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
+  cp ${cdna_t2g} ${file_prefix}/
+  cp ${intron_t2g} ${file_prefix}/
   """
   else
   """
@@ -403,5 +412,8 @@ process velocity_marseq {
     ${params.count} \
     -x 1,0,6:1,6,14:0,0,0 \
     ${reads} > ${file_prefix}_kb_mapping_report.txt
+  cp ${transcript_to_gene} ${file_prefix}/
+  cp ${cdna_t2g} ${file_prefix}/
+  cp ${intron_t2g} ${file_prefix}/
   """
 }
\ No newline at end of file
-- 
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