From 45be888a9cc7594d4d36d01e47b86efa350b3096 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 2 Jul 2021 15:46:47 +0200
Subject: [PATCH] mlepetit/nextflow-Maxime
---
src/nf_modules/kb/main.nf | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 0f3986c7..3668b7b3 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -145,6 +145,7 @@ process kb_default {
-o ${file_prefix} \
${whitelist_param} \
-x 10XV3 \
+ --h5ad \
${params.count} \
${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
cp ${transcript_to_gene} ${file_prefix}/
@@ -195,6 +196,7 @@ process kb_marseq {
-o ${file_prefix} \
${whitelist_param} \
${params.count} \
+ --h5ad \
-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}/
@@ -210,6 +212,7 @@ process kb_marseq {
${whitelist_param} \
${params.count} \
-x 1,0,6:1,6,14:0,0,0 \
+ --h5ad \
${reads} > ${file_prefix}_kb_mapping_report.txt
cp ${transcript_to_gene} ${file_prefix}/
"""
@@ -337,6 +340,7 @@ process velocity_default {
--workflow lamanno \
${whitelist_param} \
-x 10XV3 \
+ --h5ad \
${params.count} \
${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
cp ${transcript_to_gene} ${file_prefix}/
@@ -390,6 +394,7 @@ process velocity_marseq {
-c1 ${cdna_t2g} \
-c2 ${intron_t2g} \
--workflow lamanno \
+ --h5ad \
${whitelist_param} \
${params.count} \
-x 1,0,6:1,6,14:0,0,0 \
@@ -417,4 +422,5 @@ process velocity_marseq {
cp ${cdna_t2g} ${file_prefix}/
cp ${intron_t2g} ${file_prefix}/
"""
-}
\ No newline at end of file
+}
+
--
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