From 91d52f90a1e909f38c4b9c4d5ba4e50c378b887b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 21:39:43 -0600
Subject: [PATCH] Use updated input bag name
---
.gitlab-ci.yml | 6 +++---
workflow/rna-seq.nf | 2 +-
workflow/scripts/bdbagFetch.sh | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 587a25e..b63a579 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -49,8 +49,8 @@ getData:
script:
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- - unzip ./test_data/bag/staging/Q-Y5F6_inputBag.zip
- - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
+ - unzip ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag_20201228 Q-Y5F6 TEST
- pytest -m getData
artifacts:
name: "$CI_JOB_NAME"
@@ -655,7 +655,7 @@ override_inputBag:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Replicate_Q-Y5F6.zip --upload false --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b09ee5f..30f9bd1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -231,7 +231,7 @@ process getData {
echo -e "LOG: linked" >> ${repRID}.getData.log
# get bag basename
- replicate=\$(basename "${inputBag}" | cut -d "_" -f1)
+ replicate=\$(basename "${inputBag}")
echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
# unzip bag
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index 2a0ee96..606b883 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -2,7 +2,7 @@
if [ -z "${3}" ]
then
- bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag
+ bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*R*.fastq.gz")
do
path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
@@ -10,5 +10,5 @@ then
done
elif [ "${3}" == "TEST" ]
then
- bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}_inputBag
+ bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi
--
GitLab