From 8792bf4baca4c0e826aabb1306e1fb59ceff1919 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 10:27:38 -0600
Subject: [PATCH] Start changing model
---
workflow/conf/replicate_export_config.json | 2 +-
workflow/rna-seq.nf | 13 +++++++------
workflow/scripts/bdbagFetch.sh | 2 +-
3 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/workflow/conf/replicate_export_config.json b/workflow/conf/replicate_export_config.json
index ff17fa5..4380e46 100644
--- a/workflow/conf/replicate_export_config.json
+++ b/workflow/conf/replicate_export_config.json
@@ -1,6 +1,6 @@
{
"bag": {
- "bag_name": "Replicate_{rid}",
+ "bag_name": "{rid}_inputBag",
"bag_algorithms": [
"md5"
],
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 09d35d6..ccedc85 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -157,7 +157,7 @@ process getBag {
path replicateExportConfig
output:
- path ("Replicate_*.zip") into bag
+ path ("*.zip") into bag
when:
inputBagForce == ""
@@ -222,7 +222,7 @@ process getData {
echo -e "LOG: linked" >> ${repRID}.getData.log
# get bag basename
- replicate=\$(basename "${inputBag}" | cut -d "." -f1)
+ replicate=\$(basename "${inputBag}" | cut -d "_" -f1)
echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
# unzip bag
@@ -1511,10 +1511,11 @@ process outputBag {
hostname > ${repRID}.outputBag.log
ulimit -a >> ${repRID}.outputBag.log
- mkdir -p ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
- cp ${bam} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
- cp ${bigwig} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
- cp ${counts} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
+ mkdir -p ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+ cp ${bam} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+ cp ${bai} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+ cp ${bigwig} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+ cp ${counts} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:20:-1}
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index 606b883..1cab130 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -2,7 +2,7 @@
if [ -z "${3}" ]
then
- bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
+ bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag
for i in $(find */ -name "*R*.fastq.gz")
do
path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
--
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