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GUDMAP_RBK
RNA-seq
Commits
a1358467
Commit
a1358467
authored
4 years ago
by
Gervaise Henry
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Add date tail for test input bag
parent
c4865b26
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2 merge requests
!58
Develop
,
!53
Resolve "process_derivaUpload"
Pipeline
#8665
canceled with stages
in 1 hour, 3 minutes, and 38 seconds
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2
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2 changed files
.gitlab-ci.yml
+1
-1
1 addition, 1 deletion
.gitlab-ci.yml
test_data/createTestData.sh
+2
-2
2 additions, 2 deletions
test_data/createTestData.sh
with
3 additions
and
3 deletions
.gitlab-ci.yml
+
1
−
1
View file @
a1358467
...
...
@@ -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/Q-Y5F6_inputBag.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/Q-Y5F6_inputBag
_xxxxxxxx
.zip --upload
false
--ci
true
-
find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts
:
name
:
"
$CI_JOB_NAME"
...
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test_data/createTestData.sh
+
2
−
2
View file @
a1358467
...
...
@@ -13,10 +13,10 @@ ln -sfn ./test_data/auth/credential.json ~/.deriva/credential.json
mkdir
-p
./NEW_test_data/bag
singularity run
'docker://gudmaprbk/deriva1.3:1.0.0'
deriva-download-cli staging.gudmap.org
--catalog
2 ../workflow/conf/Replicate_For_Input_Bag.json
.
rid
=
Q-Y5F6
cp
Q-Y5F6_inputBag.zip ./NEW_test_data/bag/Q-Y5F6_inputBag.zip
cp
Q-Y5F6_inputBag.zip ./NEW_test_data/bag/Q-Y5F6_inputBag
_xxxxxxxx
.zip
mkdir
-p
./NEW_test_data/fastq
unzip ./NEW_test_data/bag/Q-Y5F6_inputBag.zip
unzip ./NEW_test_data/bag/Q-Y5F6_inputBag
_xxxxxxxx
.zip
singularity run
'docker://gudmaprbk/deriva1.3:1.0.0'
bash ../workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6
cp
Q-Y5F6.R1.fastq.gz ./NEW_test_data/fastq/Q-Y5F6.R1.fastq.gz
cp
Q-Y5F6.R2.fastq.gz ./NEW_test_data/fastq/Q-Y5F6.R2.fastq.gz
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